ch. 2 molecules of life book notes

carboxyl group:

COOH; a carbon atom with a double bond to oxygen and a single bond to a hydroxyl group.

nonpolar:

Describes compounds that do not have regions of positive and negative charge, hydrophobic compounds are nonpolar

unsaturated:

Describes fatty acids that contain carbon-carbon double bonds.

saturated:

Describes fatty acids that do not contain double bonds; the maximum number of hydrogen atoms is attached to each carbon atom, "saturating" the carbons with hydrogen atoms.

complementary:

Describes the relationship of purine and pyrimidine bases, in which the base A pairs only with T and G pairs only with C.

nucleotide:

A constituent of nucleic acids, consisting of a 5-carbon sugar, a nitrogen-containing base, and one or more phosphate groups.

nucleic acid:

A polymer of nucleotides that encodes and transmits genetic information.

acidic pH solution:

Describes a solution in which the concentration of protons is higher than that of hydroxide ions (the pH is lower than 7).

saccharide:

The simplest carbohydrate molecule, also called a sugar.

ionic bond:

The association of two atoms resulting from the attraction of opposite charges.

polar covalent bond:

bonds that do not share electrons equally.

hydrophobic:

"Water fearing"; describes a class of molecules poorly able to undergo hydrogen bonding with water.

hydrophilic:

"Water loving"; describes a class of molecules with which water can undergo hydrogen bonding. Hydrophilic compounds are polar; they dissolve readily in water.

All 6-carbon sugars have the same chemical formula:

(C6H12O6)

What is the maximum number of electrons in any orbital?

2

Core Concepts:

2.1 The atom is the fundamental unit of matter. 2.2 Atoms can combine to form molecules linked by chemical bonds. 2.3 Water is essential for life. 2.4 Carbon is the backbone of organic molecules. 2.5 Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units. 2.6 Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life.

After the first shell, the maximum number of electrons per energy level is?

8

glycerol:

A 3-carbon molecule with OH groups attached to each carbon. The carboxyl end of each fatty acid chain attaches to glycerol at one of the OH groups, releasing a molecule of water.

phosphodiester bond:

A bond that forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide. Phosophodiester bonds are relatively stable and form the backbone of a DNA strand. involves the loss of a water molecule.

organic molecule:

A carbon-containing molecule.

covalent bond:

A chemical bond formed by a shared pair of electrons holding two different atoms together, which is denoted by a single line connecting the two chemical symbols for the atoms

side chain:

A chemical group attached to the central carbon atom of an amino acid, whose structure and composition determine the identity of the amino acid; also known as an *R group*.

polymer:

A complex organic molecule made up of repeated simpler units connected by covalent bonds.

nonpolar covalent bond:

A covalent bond between atoms that have the same, or nearly the same, electronegativity.

double bond:

A covalent bond in which covalently joined atoms share two pairs of electrons, denoted by a double line connecting the two chemical symbols for the atoms.

Differentiate between covalent bonds and generally weaker interactions such as polar covalent, hydrogen, and ionic bonds.

A covalent bond is present when two atoms share their valence electrons (the electrons in the outermost orbital of an atom). Each shared pair of valence electrons make a covalent bond that is depicted by a single line connecting the two chemical symbols for the atoms. A polar covalent bond is present when the valence electrons are not shared equally by the two atoms, thus giving areas of the molecule a positive or negative charge. A hydrogen bond forms when a hydrogen atom covalently bound to an electronegative atom (giving the hydrogen a partial positive charge) interacts with an electronegative atom of another molecule. A hydrogen bond is typically depicted by a dotted line. An ionic bond is formed by the attraction between a molecule that has a positive charge (due to the loss of one electron) and a molecule that has a negative charge (due to the gain of one electron). The two molecules are not covalently bound, but they associate with each other due to their opposite charges.

glycosidic bond:

A covalent bond that attaches one monosaccharide to another. involves the loss of a water molecule. A glycosidic bond is formed between carbon 1 of one monosaccharide and a hydroxyl group carried by a carbon atom in a different monosaccharide molecule

peptide bond:

A covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group of another amino acid.

deoxyribonucleic acid (DNA):

A linear polymer of four subunits; the information archive in all organisms, genetic material in all organisms

triacylglycerol:

A lipid composed of a glycerol backbone and three fatty acids.

solvent:

A liquid capable of dissolving a substance.

fatty acid:

A long chain of carbons attached to a carboxyl group; three fatty acid chains attached to glycerol form a triacylglycerol, a lipid used for energy storage.

complex carbohydrate:

A long, branched chain of monosaccharides.

molecular orbital:

A merged orbital traversed by a pair of shared electrons.

ribonucleic acid (RNA):

A molecule chemically related to DNA that is synthesized by proteins from a DNA template. a key player in protein synthesis and the regulation of gene expression.

polar:

A molecule that has regions of positive and negative charge.

base:

A nitrogen-containing compound that makes up part of a nucleotide.

polysaccharide:

A polymer of simple sugars. Polysaccharides provide long-term energy storage or structural support.

enzyme:

A protein that functions as a catalyst to accelerate the rate of a chemical reaction; enzymes are critical in determining which chemical reactions take place in a cell.

element:

A pure substance, such as oxygen, copper, gold, or sodium, that cannot be further broken down by the methods of chemistry.

uracil (U):

A pyrimidine base in RNA, where it replaces the thymine found in DNA.

cytosine (C):

A pyrimidine base.

thymine (T):

A pyrimidine base.

orbital:

A region in space where an electron is present most of the time.

monosaccharide:

A simple sugar. unbranched carbon chains with either an aldehyde (HC = O) or a ketone (C = O) group. Monosaccharides with an aldehyde group are called aldoses and those with a ketone group are known as ketoses. In both types of monosaccharide, the other carbons each carry one hydroxyl (-OH) group and one hydrogen (H) atom.

molecule:

A substance made up of two or more atoms, that act as a single unit. when atoms combine to make a molecule, they share valence electrons with each other

phospholipid:

A type of lipid and a major component of the cell membrane.

hydrogen bond:

A weak bond between a hydrogen atom in one molecule and an electronegative atom in another molecule.

Name and describe the components of an atom.

An atom is made up of positively charged particles called protons, neutral particles called neutrons, and negatively charged particles called electrons. The dense central nucleus of an atom is made up of protons and neutrons. Electrons orbit around the nucleus, and the regions of space where they are most likely to be found are called orbitals.

ion:

An electrically charged atom or molecule.

carbohydrate:

An organic molecule containing C, H, and O atoms that provides a source of energy for metabolism and that forms the starting point for the synthesis of all other organic molecules.

amino acid:

An organic molecule containing a central carbon atom, a carboxyl group, an amino group, a hydrogen atom, and a side chain. Amino acids are the building blocks of proteins.

lipid:

An organic molecule that stores energy, acts as a signaling molecule, and is a component of cell membranes.

chemical bond:

Any form of attraction between atoms that holds them together.

reactant:

Any of the starting molecules in a chemical reaction.

product:

Any one of the transformed molecules that result from a chemical reaction.

cohesion:

Attraction between molecules; one consequence of cohesion is high surface tension- a measure of the difficulty of breaking the surface of a liquid. Cohesion between molecules contributes to water movement in plants.

basic pH solution:

Describes a solution in which the concentration of protons is lower than that of hydroxide ions (the pH is higher than 7).

Describe how diversity is achieved in polymers, using proteins as an example.

Diversity is achieved in polymers through endless combinations of subunits. A protein, for example, is a polymer of amino acid subunits. As we will discuss in Chapter 4, there are 20 different kinds of amino acids. Thus, there are numerous combinations of subunits that could be made, each resulting in a different protein. In this way, polymers are capable of displaying virtually limitless diversity.

How is the periodic table of the elements arranged?

Elements are arranged in rows by increasing number of protons, the increasing atomic number. The elements in a column, often called group or family, share similar chemical properties, they have the same number of electrons in their outermost shell.

List features of carbon that allow it to form diverse structures.

Features of carbon that allow it to form diverse structures are the following: A carbon atom behaves as if it has four unpaired electrons, allowing it to form covalent bonds with up to four different atoms. Each of these bonds can also rotate freely, contributing to the structural diversity of carbon-based molecules. Carbon atoms can bond with other carbon atoms to form large carbon chains that branch or form rings, also giving rise to a great diversity of structures. Carbon can also form double bonds (sharing two electrons). A double bond does not freely rotate, which limits the flexibility of the molecule and its structural options.

How is glucose different from galactose?

Glucose and galactose differ only in the orientation of the -OH and -H groups attached to carbon 4.

functional groups:

Groups of one or more atoms that have particular chemical properties of their own, regardless of what they are attached to.

From their positions in the periodic table (see Fig. 2.3), can you predict how many lithium atoms and hydrogen atoms can combine to form a molecule?

Hydrogen and lithium are in the same column, or group, in the periodic table. Each has one valence electron in their outer orbital. As a result, one atom of lithium combines with one atom of hydrogen to make lithium hydride, with a full complement of two electrons in the single molecular orbital.

Why do containers of water, milk, soda, or other liquids sometimes burst when frozen?

Ice is less dense than liquid water. As a result, when water freezes, it expands in volume and can burst closed containers, such as cans of soda or water pipes in houses. This property is unusual. For most substances, the solid phase is more dense than the liquid phase.

pyrimidine:

In nucleic acids, any of the bases thymine, cytosine, and uracil, which have a single-ring structure.

purine: In nucleic acids, either of the bases adenine and gunanine, which have a double-ring structure.

In nucleic acids, either of the bases adenine and gunanine, which have a double-ring structure.

isomers:

Molecules that have the same chemical formula but different structures.

amino group:

NH2; a nitrogen atom bonded to two hydrogen atoms, covalently linked to the central carbon atom of an amino acid.

In the early 1900s, Ernest Rutherford produced a beam of very small positive particles and directed it at a thin piece of gold foil just a few atoms thick. Most of the particles passed through the foil without changing their path; very rarely, a particle was deflected. What conclusions can you draw from this experiment about the structure of an atom?

One conclusion is that atoms consist mainly of empty space, and hence most positively charged particles passing through the gold foil do not come close enough to any other positive charge to be deflected. Another conclusion is that the positively charged protons in the nucleus must be small and densely packed.

List essential functions of proteins, nucleic acids, carbohydrates, and lipids.

Proteins act as catalysts to facilitate chemical reactions and also provide structural support of the cell. Nucleic acids encode and transmit genetic information. Carbohydrates provide a source of energy and make up the cell wall in bacteria, plant, and algae cells. Lipids store energy, act as signaling molecules, and make up the membranes of the cell.

electronegativity:

The ability of atoms to attract electrons. Electronegativity tends to increase across a row in the periodic table; as the number of protons across a row increases, electrons are held more tightly to the nucleus.

van der Waals forces:

The binding of temporarily polarized molecules because of the attraction of opposite charges.

α (alpha) carbon:

The central carbon atom of each amino acid.

valence electrons:

The electrons farthest from the nucleus, which are at the highest energy level.

hydrophobic effect:

The exclusion of nonpolar molecules by polar molecules, which drives biological processes such as the formation of cell membranes and the folding of proteins.

List the four most common elements in organic molecules and state which common macromolecules always contain all four of these elements.

The four most common elements in organic molecules in order of decreasing abundance by dry mass are carbon, oxygen, hydrogen, and nitrogen. All four of these elements are found in proteins and nucleic acids because they are parts of the building blocks of these polymers.

proteins:

The key structural and functional molecules that do the work of the cell, providing structural support and catalyzing chemical reactions. The term "protein" is often used as a synonym for "polypeptide."

pH:

The pH of a solution measures the proton concentration ([H-]), which is important as the pH influences many chemical reactions and biological processes. It is calculated by the following formula: pH = -log [H+], pH of a solution can range from 0 to 14. protons (H+). hydroxide ions (OH-)

Explain how the periodic table of the elements is organized.

The periodic table of elements is organized by the increasing atomic number of each atom. The atomic number is the number of protons an atom has in its nucleus. Hydrogen appears first in the periodic table because it has an atomic number of 1. The elements in a column share similar chemical properties, and each has the same number of electrons in its outermost orbital. Elements in a row have the same number of shells (energy levels), and thus the same number and types of orbitals.

What evidence is there for the hypothesis that life originated on Earth by the creation and polymerization of small organic molecules by natural processes?

The principal molecules found in organisms are themselves made of simpler molecules joined together. So if we want to understand how proteins emerged on Earth, then we first have to understand the synthesis of amino acids. Stanley Miller conducted experiments that showed that when a mixture of gases―which were thought to have been present in the early atmosphere―were ignited with a spark, amino acids were generated. Other scientists have subsequently shown that the other building blocks of life—sugars, bases, and lipids—can also be formed in laboratory conditions that simulate the early atmosphere. Analyses of meteorites that provide samples of the early solar system have also shown the presence of diverse amino acids, lipids, and other organic compounds, which supports Miller's initial hypothesis. Building off of Miller's work, Leslie Orgel performed experiments that showed how nucleotides would spontaneously join to synthesize nucleic acids. Many years later, John Sutherland and his colleagues were able to synthesize nucleotides themselves under conditions thought to be like those on the early Earth.

chemical reaction:

The process by which molecules are transformed into different molecules.

sugar:

The simplest carbohydrate molecule; also called a saccharide.

double helix:

The structure formed by two strands of complementary nucleotides that coil around each other.

what determines atomic mass?

Together, the protons and neutrons determine the atomic mass, the mass of the atom. The atomic mass is sometimes indicated as a superscript to the left of the chemical symbol.

List three unusual properties of water and explain why these properties make water conducive to life.

Water has unusual properties and is conducive to life in the following ways: Water is a polar molecule, and because of its regions of positive and negative charge, some molecules are attracted to water (hydrophilic) and some are repelled by it (hydrophobic). It is this property that allows things like lipid cellular membranes, and thus cells, to exist. The polar nature of water also makes it a good solvent—hydrophilic compounds dissolve readily in water. Water also has a neutral pH (around 7), the pH of most cells. Since many chemical reactions can only be carried out in a solution around a neutral pH, it is important that the cell remain in this range to function. Water resists temperature changes better than other substances due to its extensive network of hydrogen bonding. This is important for a variety of reasons. This phenomenon allows chemical reactions, which produce heat as a by-product, to occur inside the cell without changing the internal temperature. In a similar way, but on a global scale, the oceans act as a temperature regulator and keep the Earth in a temperature range that supports life. The network of hydrogen bonds that forms when water freezes makes ice less dense than liquid water. As a result, ice floats on water, which allows aquatic life to survive below the ice in the winter. Finally, the cohesive properties and surface tension of water facilitate water transportation in plants.

neutral pH solution:

a solution is neutral (pH = 7) when the concentrations of protons (H+) and hydroxide ions (OH-) are equal.

isotope:

atoms of the same element that have different numbers of neutrons.

two simple sugars linked together by a covalent bond is called a:

disaccharide

what is a hydrocarbon?

it is a molecule composed entirely of carbon and hydrogen atoms.

The atom contains a dense central nucleus made up of positively charged particles called ______ and electrically neutral particles called ________. A third type of particle, the negatively charged _________ , moves around the nucleus at some distance from it.

protons, neutrons, electrons

each element contains only one type of *atom*; which is:

the basic unit of matter.

2.4 Carbon is the backbone of organic molecules.

• A carbon atom can form up to four covalent bonds with other atoms. • The geometry of these covalent bonds helps explain the structural and functional diversity of organic molecules.

2.5 Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units.

• Amino acids are linked by covalent bonds to form proteins. • An amino acid consists of a carbon atom (the α carbon) attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain. • The side chain determines the properties of an amino acid. • Nucleotides assemble to form nucleic acids, which store and transmit genetic information. • Nucleotides are composed of a 5-carbon sugar, a nitrogen-containing base, and a phosphate group. • Nucleotides in DNA incorporate the sugar deoxyribose, and nucleotides in RNA incorporate the sugar ribose. • The bases are pyrimidines (cytosine, thymine, and uracil) and purines (guanine and adenine). • Sugars are carbohydrates, molecules composed of C, H, and O atoms, usually in the ratio 1:2:1, and are a source of energy. • Monosaccharides assemble to form disaccharides or longer polymers called complex carbohydrates. • Lipids are hydrophobic. • Triacylglycerols store energy and are made up of glycerol and fatty acids. • Fatty acids consist of a linear hydrocarbon chain of variable length with a carboxyl group at one end. • Fatty acids are either saturated (no carbon-carbon double bonds) or unsaturated (one or more carbon-carbon double bonds). • The tight packing of fatty acids in lipids is the result of van der Waals forces, a type of weak, noncovalent bond.

2.1 The atom is the fundamental unit of matter.

• Atoms consist of positively charged protons and electrically neutral neutrons in the nucleus, as well as negatively charged electrons moving around the nucleus. • The number of protons determines the identity of an atom. • The number of protons and neutrons together determines the mass of an atom. • The number of protons versus the number of electrons determines the charge of an atom. • Negatively charged electrons travel around the nucleus in regions called orbitals. • The periodic table of the elements reflects a regular and repeating pattern in the chemical behavior of elements.

2.6 Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life.

• In 1953, Stanley Miller and Harold Urey demonstrated that amino acids can be generated in the laboratory in conditions that mimic those of the early Earth. • Other experiments have shown that sugars, bases, and lipids can be generated in the laboratory. • Once the building blocks were synthesized, they could join together in the presence of clay minerals to form polymers.

2.2 Atoms can combine to form molecules linked by chemical bonds.

• Valence electrons occupy the outermost energy level (shell) of an atom and determine the ability of an atom to combine with other atoms to form molecules. • A covalent bond results from the sharing of electrons between atoms to form a molecular orbital. • A polar covalent bond results when two atoms do not share electrons equally as a result of a difference in the ability of the atoms to attract electrons, a property called electronegativity. • An ionic bond results from the attraction of oppositely charged ions.

2.3 Water is abundant and essential for life.

• Water is a polar molecule because shared electrons are distributed asymmetrically between the oxygen and hydrogen atoms. • Hydrophilic molecules dissolve readily in water, whereas hydrophobic molecules in water tend to associate with one another, minimizing their contact with water. • A hydrogen bond results when a hydrogen atom covalently bonded to an electronegative atom interacts with an electronegative atom of another molecule. • Water forms hydrogen bonds, which help explain its high cohesion, surface tension, and resistance to rapid temperature change. • The pH of an aqueous solution is a measure of the acidity of the solution.