Science Shepherd Biology Chapter 3 Vocabulary

Front 1

organic compounds
or
organic molecules
or
carbon compounds

Back 1

1. Organic compounds are complex molecules synthesized or made by all life forms.
2. Organic compounds are formed with a carbon backbone.
3. Organic molecules always contain carbon and hydrogen and many contain oxygen.
4. Because of the structural importance of carbon in organic molecules, the term "carbon compound" is also used.
5. Carbon is the basic atom of life due to its electron orbital structure. Carbon has 6 protons, 6 electrons, and 6 neutrons.
6. Carbon has 2 electrons in the first electron shell and 4 electrons in the second electron shell. Carbon bonds with four other atoms to fill the orbital shell according to the octet rule.
7. Since carbon can bond to 4 other atoms, a variety of bonding patterns occur that allow isomers to form.
8. Carbon's properties allow carton to bond in a (1) straight line, (2) branched, or even (3) a ring structure.

Four Classes of Organic Molecules: Carbohydrates, Lipids, Proteins, Nucleic Acids
Organic Compound = Carbon + Hydrogen, and sometimes Oxygen

Organic vs. Inorganic Molecules:
1. Organic molecules are large with many atoms; inorganic molecules are small.
2. Organic molecules always make covalent bonds; inorganic molecules usually make ionic bonds.
3. Organic molecules always contain carbon; inorganic molecules do not contain carbon.
4. Organic molecules always contain bonds between carbon and hydrogen; inorganic molecules never have bonds between carbon and hydrogen.

Organic molecule example: sugar
Inorganic molecule example: silicon for computer chips, LCD screens, and fiber optics.

Hint 1

3.1
3.2
3.3
3.8

Front 2

organic chemistry

Back 2

1. Organic chemistry is the study of the principles of organic compounds; it is the course of study where biology and chemistry come together.
2. Organic chemistry deals with the role carbon, hydrogen, and oxygen molecules play in maintaining the life and energy cycle.
3. Building an organic molecule begins with photosynthesis when sugars are made from the energy of the sun, carbon atoms from carbon dioxide, and oxygen and hydrogen atoms from water.

Hint 2

3.2

Front 3

four classes of organic molecules

Back 3

ATP energy molecules are used to drive all chemical reactions within the cells to make the four classes of organic molecules:
Carbohydrates - Lipids - Proteins - Nucleic Acids

Hint 3

3.2

Front 4

molecular formula
or
chemical formula

Back 4

1. A molecular or chemical formula is an accounting of the number and type of atoms in a molecule. ie. H₂O is the formula for one molecule of water.
2. Because organic molecules are so large and complex, the molecular/chemical formula may be used by different molecules with the same type and number of atoms. ie. butane and isobutane have the same molecular/chemical formula C₄H₁₀ but figure 3.4.1 shows their different structures.

Hint 4

3.4

Front 5

isomer
isomerization

Back 5

1. Molecules with the same simple chemical formula, but different structural formulae are isomers. ie. butane and iso-butane.
2. Isomerization is the formation of multiple molecules with the same chemical formula but different structural formulae.
3. Isomers have different physical, as well as chemical, properties because they have different structures. ie. butane and isobutane have different boiling points based on their differing three-dimensional structures.

Hint 5

3.4
3.5
3.6

Front 6

structural formula

Back 6

1. The structural formula represents a molecule showing the relationship of bonds to atoms.
2. The structural formula shows a flat, two-dimensional bonding pattern between atoms even though atoms are really three-dimensional.
3. The structural formula is preferred in the study of organic chemistry because it provides more detail on bonding patterns than the molecular formula.

Hint 6

3.4
3.5
3.6

Front 7

bonding pattern:
(single) covalent bond
double covalent bond
triple covalent bond

Back 7

1. When writing structural formulae, atoms bonded together are shown with lines drawn between them.
2. Each line shows two atoms sharing one electron pair.
3. This is represented as 1, 2, or 3 lines drawn between atoms in the structural model.

covalent bond - A bond in which 1 pair of electrons are shared between two atoms. Represented by 1 line drawn between atoms in the structural model.
double covalent bond - A bond in which 2 pairs of electrons are shared between two atoms. Represented by 2 lines drawn between atoms in the structural model.
triple covalent bond - A bond in which 3 pairs of electrons are shared between two atoms. Represented by 3 lines drawn between atoms in the structural model.

Hint 7

3.7

Front 8

organic reactions
or
anabolic reactions - synthesis
or
catabolic reactions - hydrolysis

Back 8

1. Organisms use organic reactions to build - or synthesize- organic molecules in anabolic reactions.
2. Organisms use organic reactions to break organic molecules into smaller pieces - to hydrolyze organic molecules into smaller pieces - in catabolic reactions.

OPPOSITES
synthesize - hydrolyze
synthesis - hydrolysis
anabolic reaction - catabolic reaction

Hint 8

3.9

Front 9

synthesize
synthesis

Back 9

1. Synthesize means to build (verb). Synthesis is what is built together (noun).
2. Organisms synthesize, or build, larger molecules (polymers) from smaller molecule precursors (monomers) or smaller molecule parts.
3. The opposite of synthesis is hydrolysis in organic chemistry. Synthesis builds ups; hydrolysis takes away or makes smaller.

Hint 9

3.1
3.9
3.10
3.11

Front 10

monomer

Back 10

1. All organic molecules start as tiny molecules called monomers.
2. Monomers are the building blocks of organic molecules.
3. Monomers are linked together to form larger molecules.
4. Anabolic reactions link [or synthesize] one monomer to another to form larger polymer molecules.
5. Monomers may be obtained by breaking down [by hydrolysis] the larger polymer molecules through catabolic reactions.

Hint 10

3.10

Front 11

polymer

Back 11

A polymer is a large molecule formed by repeatedly linking monomers together through anabolic reactions.

Hint 11

3.10

Front 12

macromolecule

Back 12

1. A macromolecule is a very, very, very large polymer. ie. DNA and RNA
2. Large carbohydrate macromolecules include glycogen, cellulose, and starch.

Hint 12

3.10
3.19

Front 13

dehydration synthesis reaction
or
condensation reaction

Back 13

1. The anabolic reaction used by organisms to build carbohydrates, proteins, nucleic acids, and lipids (among others) is called dehydration synthesis.
2. Dehydration reactions are also called condensation reactions because water is always removed during the reaction making water a product of the reaction.
3. This occurs as a hydrogen ion (H⁺) from one monomer and a hydroxide ion (OH⁻) from another monomer are removed to form a water molecule (H₂O). The ends of the molecules where the hydrogen and hydroxide ions were removed are linked or bonded to form a new, larger molecule.
4. The dehydration process may be repeated tens, hundreds, and even thousands of times on the same molecule.
5. Each time a dehydration synthesis reaction is performed, a monomer is added to the growing polymer.
6. An organism builds bigger sugar polymers [polysaccharides] from smaller monomer units through dehydration synthesis reactions.

Hint 13

3.11
3.16

Front 14

hydrolysis reaction
or
hydration reaction

Back 14

1. The catabolic reaction used by organisms to remove monomers from organic molecules [polymers] one at a time is hydrolysis or hydration.
2. Water is one of the reactants in a hydrolysis or hydration reaction. ie. hydra (hydro) = water
3. A hydrolysis reaction is performed by adding water (H₂O) to the polymer at a specific location. The cell utilizes the water and breaks it into the hydrogen (H⁺) and hydroxide (OH⁻) ions. The bond on the polymer is broken and filled in by the ions, releasing the monomer as the product of the hydrolysis/hydration reaction.
4. The hydrolysis/hydration process can occur multiple times in order to break the molecule down as much as is needed by the organism.
5. Each time a dehydration synthesis reaction occurs, one monomer is removed from the polymer.

Hint 14

3.10
3.12

Front 15

carbohydrate
or
sugar
or
saccharide

Back 15

1. Carbohydrates are sugars.
2. Saccharide is the scientific name for sugars/carbohydrates of any size.
3. Sugars/carbohydrates are the universal fuel for all cell functions. Lipids and proteins can be used if absolutely necessary [as in starvation], but result in damage to the organism [as in muscle loss].
4. The first and best source of fuel comes from sugars/carbohydrates.
5. Carbohydrates are synthesized by the cell.
6. Most carbohydrate names end in "-ose".
7. Carbohydrates are only made up of carbon, hydrogen, and oxygen.
8. Carbohydrates have two hydrogen atoms for every oxygen atom.
9. General chemical formula to indicate a carbohydrate is CH₂O, even though the number and orientation of the carbon atoms determine the specific sugar in the structural formula.

Hint 15

3.2
3.13

Front 16

monosaccharide

Back 16

1. A monosaccharide is the most basic form or monomeric building unit of carbohydrates. Carbohydrates are polymers of monosaccharides.
2. A monosaccharide is a saccharide that contains between 3 and 7 carbon atoms per molecule.
3. Common monosaccharides are the isomers glucose [sugar used by animals as fuel source] and fructose [plant sugar that makes many fruits sweet] with the shared molecular formula C₆H₁₂O₆.
4. Monosaccharides usually exist in the cyclic [ring] form and but may also be in a straight chain.

Hint 16

3.14
3.15

Front 17

glycosidic bond

Back 17

1. A glycosidic bond results from the dehydration synthesis reaction to form polysaccharides.
2 The new molecule is always held together with an oxygen molecule in the middle as a bridge to a carbon on each saccharide unit. This bridge is the glycosidic bond.
3. It involves a bond of C-O-C.
4. A glycosidic bond is broken by a hydrolysis reaction. When water is added, the molecules held together by the glycosidic bond are broken apart.

Hint 17

3.16
3.17

Front 18

disaccharide

Back 18

1. A disaccharide is a molecule formed through a dehydration synthesis reaction to link together only two monosaccharides with a glycosidic bond.
2. An example occurs when one glucose and one fructose molecules go through the anabolic condensation synthesis [or dehydration synthesis] reaction to make the disaccharide sucrose.
3. Common disaccharides include (1) sucrose [table sugar], (2) maltose [common sugar for making beer from two glucose monosaccharides], and (3) lactose [sugar in dairy products made from a glucose and galactose monosaccharide molecules].

Hint 18

3.16
3.17

Front 19

polysaccharide

Back 19

1. A polysaccharide is a large sugar/carbohydrate molecule formed by repeated hydration synthesis reactions linking monosaccharides with glycosidic bonds making a polysaccharide chain.
2. Amylose is a polysaccharide commonly used in plants as a storage form of carbohydrates that the plant can later break down and use for fuel. It may be linked in a chain of 60 units or more.

Hint 19

3.18

Front 20

carbohydrate macromolecule

Back 20

1. Large carbohydrate macromolecules include glycogen, cellulose, and starch.
2. Glycogen is the main form of carbohydrate storage in animals and is abundant in the liver and skeletal muscles. Glycogen is formed from hundreds of glucose molecules. When needed glycogen is broken down and used for energy.
3. Starch accounts for about 50% of carbohydrate calories eaten by humans and is abundant in plants. Starch is formed by hundreds of amylose and amylopectin molecules linked together with glycosidic bonds.
4. Cellulose is a plant structural carbohydrate polymer [ie. builds the plant]. Cellulose is the MOST ABUNDANT organic molecule on earth.

Hint 20

3.19

Front 21

starch

Back 21

Starch is a sugar polymer used as a storage molecule in plants.

Hint 21

3.19

Front 22

lipid

Back 22

1. Lipids are organic molecules made up of many carbon and hydrogen atoms, with fewer oxygen atoms than carbohydrates.
2. Lipids are structurally more complex than carbohydrates.
3. Lipids includes fats, waxes, oils, triglycerides, and steroids.
4. Lipids are used for insulation and as a fuel source. Lipids may also be used for cooking.
5. Lipid molecules are not soluble in water, unlike carbohydrate and protein molecules.
6. The backbone of a lipid molecule is glycerol.
7. Lipids are formed by glycerol and fatty acids linked together by dehydration synthesis reaction.

Hint 22

3.2
3.20
3.21
3.22

Front 23

fatty acid

Back 23

1. A fatty acid is a long carbon chain with a carboxylic acid group on one end of the molecule.
2. Fatty acids are building block of lipids/fats.

Hint 23

3.21
3.22

Front 24

carboxylic acid group
or
carboxyl group

Back 24

1. A carboxylic acid group- or carboxyl group- is one carbon atom, two oxygen atoms, and one hydrogen atom bonded together. It is chemically written as COOH.
2. The carboxylic acid group is on the end of a fatty acid chain.

Hint 24

3.21
3.22

Front 25

saturated fatty acid
or
unsaturated fatty acid

Back 25

1. Fatty acids occur in two forms: saturated and unsaturated.
2. Saturation refers to how "saturated" the fatty acid is with hydrogen atoms.
3. A saturated fatty acid has many hydrogen atoms and no double bonds between the carbon atoms.
4. An unsaturated fatty acid has fewer hydrogen atoms and many more double bonds between the carbon atoms.
5. Most saturated fats/lipids come from animals. Saturated fat is solid at room temperature, like butter.
6. Most unsaturated fats/lipids come from plants and some fish, like salmon.
7. Generally speaking saturated fats may lead to higher blood pressure and unsaturated fats may lead to lower blood pressure in humans.

Hint 25

3.21

Front 26

glycerol

and

monoglyceride
diglyceride
triglyceride

Back 26

1. Glycerol is the building block or backbone molecule of lipids/fats with three carbon atoms bonded together with a hydroxide group (OH⁻) on each carbon atom.
2. A lipid or fat molecule is formed by linking between one and three fatty acid molecules to one glycerol molecule in a dehydration/condensation synthesis reaction, resulting in one lipid molecule and one water molecule.
3. The bond formed while producing a lipid molecule through the dehydration synthesis reaction is an ester bond.
4. The number of fatty acids attached to the glycerol backbone by ester bonds corresponds to the fat/lipid's name: monoglyceride has one fatty acid; diglyceride has two fatty acids; triglyceride has three fatty acids. Read food labels or google each word to see which foods contain each glyceride.

Hint 26

3.22

Front 27

ester bond

Back 27

1. The ester bond forms the lipid by joining the hydroxyl group (OH⁻) of glycerol and carboxylic acid group of a fatty acid.
2. Lipids are formed by ester bonds, just as sugar/saccharides are formed by glycosidic bonds.

Hint 27

3.22

Front 28

protein

Back 28

1. Proteins are important structural [building] molecules of all living organisms.
2. Proteins are structurally diverse and complex organic molecules containing not only carbon, oxygen, and hydrogen, but also other atoms such as nitrogen and sulfur.
3. Special types of proteins called enzymes run all biochemical reactions in a cell.
4. Most protein molecules are extremely large.
5. Like carbohydrates and lipids, proteins are built one molecule at a time.
6. Proteins are synthesized from monomers called amino acids.
7. Proteins are synthesized through dehydration synthesis reactions where a peptide bond is formed between carbon and nitrogen and water is given off.

Hint 28

3.2
3.23
3.24
3.25
3.26

Front 29

enzyme

Back 29

Enzymes are special types of proteins responsible for running all biochemical reactions in a cell.

Hint 29

3.23

Front 30

amino acid

Back 30

1. Amino acids are the basic monomeric unit of protein.
2. Twenty-one amino acids have been identified. These build all protein.
3. Each amino acid is formed by a central carbon atom attached to a carboxylic acid group (COOH) [like lipids], a hydrogen atom, an amino group (NH₃⁺), and the "R" group for "rest of the molecule." The R group is very important, making all 21 amino acids different from one another.

Hint 30

3.24
3.25
3.26

Front 31

peptide bond

Back 31

1. The peptide bond joins amino acids together to synthesize proteins.
2. The peptide bond is formed by a dehydration synthesis reaction that bonds a carbon atom from one amino acid to a nitrogen atom in a second amino acid.

Hint 31

3.25

Front 32

di-peptide

Back 32

A protein made up of only two amino acids is a di-peptide.

Hint 32

3.26

Front 33

polypeptide

Back 33

1. As a protein molecule grows larger and larger through multiple peptide bonds, which are the result of many condensation or dehydration synthesis reactions, it is called a polypeptide.
2. A polypeptide may be as large as several thousand amino acids bonded together.

Hint 33

3.26

Front 34

nucleic acid

Back 34

1. Nucleic acids are large, specialized organic molecules, but not as complex as some of the larger proteins.
2. Nucleic acids are polymers or macromolecules composed of nucleotides.
3. Nucleic acids are several thousand monomers [nucleotides] long, while some are millions of monomers in size.
4. Nucleic acids are like the library of the cell, containing the information (1) which tells the cell how to reproduce and (2) how to make all of the molecules the cell needs.

Hint 34

3.27
3.28
3.29
3.30

Front 35

nucleotide

Back 35

1. A nucleotide is the monomeric unit of nucleic acids.
2. Nucleotides are composed of three sub-units:
--(1) a central 5-carbon sugar called a pentose
--(2) a phosphate group linked to the pentose
--(3) a nitrogenous base linked to pentose opposite the phosphate group.
3. Common nucleic acids are DNA, RNA, and ATP.

Hint 35

3.2
3.28
3.29

Front 36

pentose

Back 36

1. A pentose is a 5-carbon sugar.
2. A pentose is the central anchor molecule in a nucleotide.
3. Deoxyribose is the pentose in DNA; ribose is the pentose in RNA, and ATP.

Hint 36

3.28
3.29
3.30
3.31

Front 37

phosphate group

Back 37

A molecule with 3 oxygen atoms linked to 1 phosphorous atom.

Hint 37

3.28

Front 38

nitrogenous base

Back 38

1. A nitrogenous base is simply a molecule group which contains nitrogen and has a basic pH [not an acid pH].
2. A nitrogenous base is a nitrogen-containing group bonded to the pentose of the nucleotide.

4 DNA bases = adenine, cytosine, thymine, guanine ACTG
4 RNA bases = adenine, cytosine, uracil, guanine ACUG
1 ATP base = adenine A

Hint 38

3.28
3.29
3.30
3.31

Front 39

DNA
deoxyribosenucleic acid

Back 39

1. DNA is a nucleic acid macromolecule containing genetic information that tells the cell (1) how to function properly, (2) how to reproduce itself, and (3) how to build proteins.
2. Each DNA nucleotide contains a phosphate group, a pentose [deoxyribose], and one of four nitrogenous bases:
--------- A - adenine
--------- C - cytosine
--------- T - thymine
--------- G - guanine
3. Each DNA nucleotide is named for the one of four A-C-T-G nitrogenous bases it contains.
4. DNA is made by repeated linking of the four nucleotides in sequences up to several million nucleotides long.
5. DNA is built as a double-stranded helix structure, like a spiral staircase.

Hint 39

3.29

Front 40

deoxyribose

Back 40

Deoxyribose is the pentose used in DNA.

Hint 40

3.29

Front 41

RNA
ribonucleic acid

Back 41

1. RNA is the nucleic acid molecule responsible for protein synthesis.
2. RNA (1) carries the instructions from DNA to the protein-making machinery of the cell indicating which protein is to be made and how to make it. RNA (2) carries the proper amino acid to the building machinery of the cell.
3. Each RNA nucleotide contains a phosphate group, a pentose [ribose], and one of four nitrogenous bases:
--------- A - adenine
--------- C - cytosine
--------- U - uracil [instead of thymine in DNA]
--------- G - guanine
4. RNA is not a macromolecule like DNA but is still a large molecule.
5. RNA is made up of four nucleotides like DNA. RNA shares three nucleotides with DNA.
5. Each RNA nucleotide is named for the one of four A-C-U-G nitrogenous bases it contains.

Hint 41

3.30

Front 42

ribose

Back 42

Ribose is the pentose used by RNA and ATP.

Hint 42

3.30
3.31

Front 43

ATP
or
adenosine triphosphate

Back 43

1. Consumers and producers convert sugars [the universal food] into ATP energy molecules [the universal energy source] during cellular respiration.
2. Each ATP nucleotide contains 3 phosphate groups [tri-phospate], a pentose [ribose], and the nitrogenous base adenine. ATP gets its name from its parts.
3. ATP energy molecules are used to drive all chemical reactions within the cells to make the four classes of organic molecules: Carbohydrates, Proteins, Lipids, Nucleic Acids
4. ATP is used to form more ATP.

ATP = cell fuel

Hint 43

3.2
3.31

Front 44

PEOPLE OF SCIENCE
Freidrich Wohler
(1800 - 1882)
First to make organic compound in the laboratory.

Back 44

1. Freidrich Wohler was a pioneer in organic chemistry.
2. Freidrich Wohler was the first to make an organic compound [urea] in the laboratory, disproving belief that only organisms could synthesize organic compounds. He did this while working in Denmark.
3. This discovery made Freidrich Wohler famous, leading to his becoming a professor at home in Germany.
4. Freidrich Wohler advanced the study of benzoic acid and metabolism.
5. Freidrich Wohler was the first to isolate two elements: aluminum and beryllium.
6. Freidrich Wohler developed a method to prepare phosphorus still in use today.

Hint 44

3.32

Front 45

#1 Key Chapter Point

Back 45

Organic molecules always contain carbon and hydrogen, and often contain oxygen. [3.2]

Hint 45

3.33

Front 46

#2 Key Chapter Point

Back 46

Because of isomers, writing the structural formula for a molecule is preferred over the simple chemical [molecular] formula, especially for organic molecules. [3.3 - 3.7]

Hint 46

3.33

Front 47

#3 Key Chapter Point

Back 47

Carbon has many unique properties which makes it specially suited to serve as the main atom [backbone] in organic molecules. [3.8]

Hint 47

3.33

Front 48

#4 Key Chapter Point

Back 48

Polymers are built from monomers using dehydration [condensation] synthesis reactions. [3.9 - 3.11]

Hint 48

3.33

Front 49

#5 Key Chapter Point

Back 49

Polymers can be broken into their smaller monomer units using hydrolysis reactions. [3.12]

Hint 49

3.33

Front 50

#6 Key Chapter Point

Back 50

Carbohydrates are built from monosaccharide monomers through the glycosidic bond. [3.13 - 3.19]

Hint 50

3.33

Front 51

#7 Key Chapter Point

Back 51

Lipids are built by linking up to three fatty acids to a backbone molecule of glycerol using the ester bond. [3.20 - 3.22]

Hint 51

3.33

Front 52

#8 Chapter Point

Back 52

Proteins are built from amino acid monomers through the peptide bond. [3.23 - 3.26]

Hint 52

3.33

Front 53

#9 Chapter Point

Back 53

Nucleic acids are built from nucleotides. [3.27 - 3.31]

Hint 53

3.33