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MOLECULES of life

Chapter Outline

Molecules of Life1

impacts, issues: Fearsome Fats

Atoms and Elements

Elements are fundamental forms of matter

Atoms are composed of smaller particles

Isotopes are varying forms of atoms

Radioisotopes may help diagnose disease and save lives

HOW much are you worth?

Chemical Bonds: How atoms interact

Atoms interact through their electrons

Chemical bonds join atoms

Atoms can combine into molecules

important Bonds in biological molecules

An ionic bond joins atoms that have opposite charges

In a covalent bond, atoms share electrons

A hydrogen bond is a weak bond between polar molecules

Water: Indispensable for life

Hydrogen bonding makes water liquid

Water can absorb and hold heat

Water is a biological solvent

How Antioxidants protect cells

acids, bases, and buffers: body fluids in flux

The pH scale indicates the concentration of hydrogen ions in fluids

Acids give up H+ and bases accept H+

A salt releases other kinds of ions

Buffers protect against shifts in pH

MOLECULES OF LIFE

Biological molecules contain carbon

Carbon’s key feature isversatile bonding

Functional groups affect the chemical behavior of organic compounds

Cells have chemical tools to assemble and break apart biological molecules

Carbohydrates: plentiful and varied

Simple sugars—the simplest carbohydrates

Oligosaccharides are short chains of sugar units

Polysaccharides are sugar chains that store energy

Lipids: fats and their chemical kin

Fats are energy-storing lipids

Phospholipids are key building blocks of cell membranes

Cholesterol and steroids anre built from sterols

PROTEINS: BIOLOGICAL MOLECULES WITH MANY ROLES

Proteins are built from amino acids

The sequence of amino acids is a protein’s primary structure

A PROTEIN’S Shape and Function

Proteins fold into complex shapes that determine their function

A proteins mayhave more than one polypeptide chain

Glycoproteins have sugars attachedand lipoproteins have lipids

Disrupting a protein’s shape denatures it

nucleotides and nucleic acids

Nucleotides areenergy carriers and have other roles

Nucleic acids include DNA and RNAs

food production and a chemical arms race

SUMMARY

Review questions

self-quiz

critical thinking

explore on your own

Molecules of Life1

Objectives

  1. Understand how protons, electrons, and neutrons are arranged into atoms and ions.
  2. Explain how the distribution of electrons in an atom or ion determines the number and kinds of chemical bonds that can be formed.
  3. Know the various types of chemical bonds, the circumstances under which each forms, and the relative strengths of each type.
  4. Understand the essential chemistry of water and of some common substances dissolved in it.
  5. Understand how small organic molecules can be assembled into large macromolecules by condensation. Understand how large macromolecules can be broken apart into their basic subunits by hydrolysis.
  6. Recognize that molecules can dissociate, and particular understand the role of acids and bases.
  7. Know the general structure of a monosaccharide with six carbon atoms, glycerol, a fatty acid, an amino acid, and a nucleotide.
  8. Know the macromolecules into which these essential building blocks can be assembled by condensation.
  9. Know where these carbon compounds tend to be located in cells or organelles and the activities in which they participate.

Key Terms

The Chemistry of Life1

atom

isotope

radioisotope

tracer

chemical bond

molecule

compound

mixture

ion

ionic bond

covalent bond

hydrogen bond

free radicals

antioxidant

hydrophilic

hydrophobic

solvent

solute

hydrogen ions, H+

hydroxide ions, OH¯

pH scale

acidbase

alkaline

buffer system

salts

organic compound

functional group

enzymes

condensation reaction

polymer

monomers

hydrolysis

carbohydrates

monosaccharides

oligosaccharides

polysaccharides

lipid

fats

fatty acid

triglycerides

phospholipid

sterols

protein

amino acid

polypeptide chain

lipoproteins

glycoproteins

denature; denaturation

nucleotide

ATP

coenzymes

nucleic acids

DNA (deoxyribonucleic acid)

RNA (ribonucleic acid)

Molecules of Life1

Lecture Outline

Impacts, Issues:Fearsome Fats

  1. Fat is essential for humans, but we generally consume far too much.
  2. Certain types of fats, such as trans fats, are particularly damaging to our health.

2.1Atoms and Elements

  1. Elements are fundamental forms of matter.
  2. Elements, mostly carbon, oxygen, hydrogen and nitrogen, make up all living things.
  3. Elements are made of atoms.
  4. Atoms are composed of smaller particles.
  5. An atom is the smallest unit of matter that is unique to a particular element.
  6. Atoms are composed of three particles:
  7. Protons (p+) are part of the atomic nucleus and have a positive charge. Their quantity is called the atomic number (unique for each element).
  8. Electrons (e¯) have a negative charge. Their quantity is equal to that of the protons. They move around the nucleus.
  9. Neutrons are also a part of the nucleus; they are neutral. Protons plus neutrons = atomic mass number.
  10. Electron activity is the basis for organization of materials and the flow of energy in living things.
  11. Isotopes are varying forms of atoms.
  12. Atoms with the same number of protons (e.g., carbon has six) but a different number of neutrons (carbon can have six, seven, or eight) are called isotopes (12C, 13C, 14C).
  13. Some radioactive isotopes are unstable and tend to decay into more stable atoms.
  14. They can be used to date rocks and fossils.
  15. Some can be used as tracers to follow the path of an atom in a series of reactions or to diagnose disease.
  16. Radioisotopes may help diagnose disease and save lives.
  17. Radioisotopes have many important uses in medicine.
  18. Tracers are substances containing radioisotopes that can be injected into patients to study tissues or tissue function.
  19. Radiation therapy uses the radiation from isotopes to destroy or impair the activity of cells that do not work properly, such as cancer cells.
  20. For safety, clinicians usually use isotopes with short half-lives (the time it takes the isotope to decay to a more stable isotope).

2.2How Much are you Worth?

  1. From a chemical perspective, human beings are not very expensive.

2.3Chemical Bonds: How Atoms Interact

  1. Atoms interact through their electrons.
  2. In chemical reactions, an atom can share electrons with another atom, accept extra electrons, or donate electrons.
  3. Electrons are attracted to protons, but are repelled by other electrons.
  4. Orbitals can be thought of as occupying shells around the nucleus, representing different energy levels.
  5. Chemical bonds join atoms.
  6. A chemical bond is a union between the electron structures of atoms.
  7. Having a filled outer shell is the most stable state for atoms.
  8. The shell closest to the nucleus has one orbital holding a maximum of two electrons.
  9. The next shell can have four orbitals with two electrons each for a total of eight electrons.
  10. Atoms with “unfilled” orbitals in their outermost shell tend to be reactive with other atoms—they want to “fill” their outer shell with the maximal eight electrons allowed.
  11. Atoms can combine into molecules.
  12. Molecules may contain more than one atom of the same element; N2 for example.
  13. Compounds consist of two or more elements in strict proportions.
  14. A mixture is an intermingling of molecules in varying proportions.

2.4Important Bonds in Biological Molecules

  1. An ionic bond joins atoms that have opposite electricalcharges.
  2. When an atom loses or gains one or more electrons, it becomes positively or negatively charged—an ion.
  3. In an ionic bond, (+) and (–) ions are linked by mutual attraction of opposite charges, for example, NaCl.
  4. In a covalent bond, atoms share electrons.
  5. A covalent bond holds together two atoms that share one or more pairs of electrons.
  6. In a nonpolar covalent bond, atoms share electrons equally; H2 is an example.
  7. In a polar covalent bond, because atoms share the electron unequally, there is a slight difference in charge (electronegativity) between the two atoms participating in the bond; water is an example.
  8. A hydrogen bond is a weak bond between polar molecules.
  9. In a hydrogen bond, a slightly negative atom of a polar molecule interacts weakly with a hydrogen atom already taking part in a polar covalent bond.
  10. These bonds impart structure to liquid water and stabilize nucleic acids and other large molecules.

2.5Water: Indispensable for Life

  1. Hydrogen bonding makes water liquid.
  2. Water is a polar molecule because of a slightly negative charge at the oxygen end and a slightly positive charge at the hydrogen end.
  3. Water molecules can form hydrogen bonds with each other.
  4. Polar substances are hydrophilic (water loving); nonpolar ones are hydrophobic (water dreading) and are repelled by water.
  5. Water can absorb and hold heat.
  6. Water tends to stabilize temperature because it has a high heat capacity—the ability to absorb considerable heat before its temperature changes.
  7. This is an important property in evaporative and freezing processes.
  8. Water is abiological solvent.
  9. The solvent properties of water are greatest with respect to polar molecules because “spheres of hydration” are formed around the solute (dissolved) molecules.
  10. For example, the Na+ of salt attracts the negative end of water molecules, while the Cl¯ attracts the positive end.

2.6How Antioxidants Protect Cells

  1. Free radicals are formed by the process of oxidation.
  2. Oxidation is the process whereby an atom or molecule loses one or more electrons.
  3. Oxidation can produce free radicals that may “steal” electrons from other molecules.
  4. In large numbers, free radicals can damage other molecules in a cell, such as DNA.
  5. Antioxidants are chemicals that can give up an electron to a free radical before it does damage to a DNA molecule.

2.7Acids, Bases, and Buffers: Body Fluids in Flux

  1. The pH scale indicates the concentration of hydrogen ions in fluid.
  2. pH is a measure of the H+ concentration in a solution; the greater the H+ the lower the value on the pH scale.
  3. The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).
  4. Acids give up H+ and bases accept H+.
  5. A substance that releases hydrogen ions (H+) in solution is an acid—for example, HCl.
  6. Substances that release ions such as (OH¯) that can combine with hydrogen ions are called bases (example: baking soda).
  7. High concentrations of strong acids or bases can disrupt living systems both internal and external to the body.
  8. A salt releases other kinds of ions.
  9. A salt is an ionic compound formed when an acid reacts with a base; example: HCl + NaOH  NaCl + H2O.
  10. Many salts dissolve into ions that have key functions in the body; for example, Na, K, and Ca in nerve and muscles.
  11. Buffers protect against shifts in pH.
  12. Buffer molecules combine with, or release, H+ to prevent drastic changes in pH.
  13. Bicarbonate is one of the body’s major buffers.

2.8Molecules of Life

  1. Biological molecules contain carbon.
  2. Only living cells synthesize the molecules characteristic of life—carbohydrates, lipids, proteins, and nucleic acids.
  3. These molecules are organic compounds, meaning they consist of atoms of carbon and one or more other elements, held together by covalent bonds.
  4. Carbon’s key feature isversatile bonding.
  5. Living organisms are mostly oxygen, hydrogen, and carbon.
  6. Much of the hydrogen and oxygen are linked as water.
  7. Carbon can form four covalent bonds with other atoms to form organic molecules of several configurations.
  8. By definition a hydrocarbon has only hydrogen atoms attached to a carbon backbone.
  9. Functional groups affect the chemical behavior of organic compounds.
  10. Functional groups—atoms or groups of atoms covalently bonded to a carbon backbone—convey distinct properties, such as solubility, to the complete molecule.
  11. Cells have chemical tools to assemble and break apart biological molecules.
  12. Enzymes speed up specific metabolic reactions.
  13. In condensation reactions, one molecule is stripped of its H+; another is stripped of its OH¯.
  14. The two molecule fragments join to form a new compound; the H+ and OH¯ form water (dehydration synthesis).
  15. Cells use series of condensation reactions to build polymers out of smaller monomers.
  16. In hydrolysis reactions, the reverse happens: one molecule is split by the addition of H+ and OH¯ (from water) to yield the individual components.

2.9Carbohydrates: Plentiful and Varied

  1. Simple sugars arethe simplest carbohydrates.
  2. A monosaccharide—one sugar unit—is the simplest carbohydrate.
  3. Sugars are soluble in water and may be sweet-tasting.
  4. Ribose and deoxyribose (five-carbon backbones) are building blocks for nucleic acids.
  5. Glucose (six-carbon backbone) is a primary energy source and precursor of many organic molecules.
  6. Oligosaccharides are short chains of sugar units.
  7. An oligosaccharide is a short chain resulting from the covalent bonding of two or three monosaccharides.
  8. Lactose (milk sugar) is glucose plus galactose; sucrose (table sugar) is glucose plus fructose.
  9. Oligosaccharides are used to modify protein structure and have a role in the body’s defense against disease.
  10. Polysaccharides are sugar chains that store energy.
  11. A polysaccharide consists of many sugar units (same or different) covalently linked.
  12. Starch (energy storage in plants) and cellulose (structure of plant cell walls) are made of glucose units but in different bonding arrangements.
  13. Glycogen is a storage form of glucose found in animal tissues.

2.10Lipids: Fats and Their Chemical Kin

Lipids are composed mostly of nonpolar hydrocarbon and are hydrophobic.

  1. Fats are energy-storing lipids.
  2. Fats are lipids that have one, two, or three fatty acids attached to glycerol.
  3. A fatty acid is a long, unbranched hydrocarbon with a carboxyl group(—COOH) at one end.
  4. Saturated fatty acids have only single C—C bonds in their tails, are solids at room temperature, and are derived from animal sources.
  5. Unsaturated fatty acids have one or more double bonds between the carbons that form “kinks” in the tails; they tend to come from plants and are liquid at room temperature.
  6. Triglycerides have three fatty acids attached to one glycerol.
  7. They are the body’s most abundant lipids.
  8. On a per-weight basis, these molecules yield twice as much energy as carbohydrates.
  9. Trans fatty acids are partially saturated (hydrogenated) lipids implicated in some types of heart disease.
  10. Phospholipids are key building blocks of cell membranes.
  11. A phospholipid has a glycerol backbone, two fatty acids, a phosphate group, and a small hydrophilic group.
  12. They are important components of cell membranes.
  13. Cholesterol and steroids are built from sterols.
  14. Steroids have a backbone of four carbon rings, but no fatty acids.
  15. Cholesterol is an essential component of cell membranes in animals and can be modified to form sex hormones.

2.11Proteins: Biological Molecules with Many Roles

Because they are the most diverse of the large biological molecules, proteins function as enzymes, in cell movements, as storage and transport agents, as hormones, as antidisease agents, and as structural material throughout the body.

  1. Proteins are built from amino acids.
  2. Amino acids are small organic molecules with an amino group, an acid group, a hydrogen atom, and one of 20varying “R” groups.
  3. They form large polymers called proteins.
  4. The sequence of amino acids is a protein’s primary structure.
  5. Primary structure is defined as the chain (polypeptide) of amino acids.
  6. The amino acids are linked together in a definite sequence by peptide bonds between an amino group of one and an acid group of another.
  7. The final shape and function of any given protein is determined by its primary structure.

2.12A Protein’s Shape and Function

Primary structure determines the shape and function of proteins by positioning different amino acids so that hydrogen bonds can form between them and by putting R groups in positions that force them to interact.

  1. Proteins fold into complex shapes that determine their function.
  2. Secondary structure is the helical coil or sheetlike array that will result from hydrogen bonding of side groups on the amino acid chains.
  3. Tertiary structure is caused by interactions among R groups, resulting in a complex three-dimensional shape.
  4. A protein may have more than one polypeptide chain.
  5. Hemoglobin, the oxygen-carrying protein in the blood, is an example of a protein with quaternary structure—the complexing of two or more polypeptide chains to form globular or fibrous proteins.
  6. Hemoglobin has four polypeptide chains (globins), each coiled and folded with a heme group at the center.
  7. Glycoproteins have sugars attached andlipoproteins have lipids.
  8. Certain proteins combine with triglycerides, cholesterol, and phospholipids to form lipoproteins for transport in the body.
  9. Glycoproteins form when oligosaccharides are added to proteins.
  10. Disrupting a protein’s shape denatures it.
  11. High temperatures or chemicals can cause the three-dimensional shape to be disrupted.
  12. Normal functioning is lost upon denaturation, which is often irreversible.

2.13Nucleotides and Nucleic Acids

  1. Nucleotides are energy carriers and haveother roles.
  2. Each nucleotide has a five-carbon sugar (ribose or deoxyribose), a nitrogen-containing base, and a phosphate group.
  3. ATP molecules link cellular reactions that transfer energy.
  4. Other nucleotides include the coenzymes, which accept and transfer hydrogen atoms and electrons during cellular reactions, and chemical messengers.
  5. Nucleic acids include DNA and the RNAs.
  6. In nucleic acids, nucleotides are bonded together to form large single- or double-stranded molecules.
  7. DNA(deoxyribonucleic acid) is double-stranded; genetic messages are encoded in its base sequences.
  8. RNA(ribonucleic acid) is single-stranded; it functions in the assembly of proteins.

2.14Food Production and a Chemical Arms Race

  1. Nearly half of the food grown each year around the world is lost to disease or insects.
  2. Natural plant defenses have been augmented by the development of synthetic toxins designed to kill pests and increase crop yields.
  3. Herbicides kill unwanted plants (weeds).
  4. Insecticides kill insects.
  5. Fungicides kill or inhibit the growth of harmful mold or fungi.
  6. Synthetic chemicals are not without dangers; some kill “good” insects and plants while others harm humans through exposure.

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