Chapter 3Chemistry of Organic Molecules

Organic Molecules

Organic chemistry—chemistry of organisms

Inorganic chemistry—chemistry of the nonliving world

Organic molecules—molecule that always contains carbon and hydrogen, and often contains oxygen as well; organic moleucles are associated with living things.

Inorganic vs. Organic MoleculesINORGANIC MOLECULES Usually contain

positive and negative ions.

Usually ionic bonding.

Always contain a small number of atoms.

Often associated with nonliving matter.

ORGANIC MOLECULES

Always contain carbon and hydrogen.

Always covalent bonding.

Often quite large, with many atoms.

Usually associated with living organisms.

Organic Molecules

4 classes of organic compounds in any living thing: Carbohydrates Lipids Proteins Nucleic acids

The Carbon Atom

Only contains 6 electrons. 2 electrons in the 1st energy level. 4 electrons in the 2nd energy level.

Carbon atom needs 4 electrons to have a complete outer energy level. It can share electrons with up to 4

different atoms.

Carbon Functional Group

Carbon chain of an organic molecule is called skeleton or backbone.

Functional group—specific combination of bonded atoms that always reacts in the same way.

Isomers

Isomers—organic molecules that have identical molecular formulas but a different arrangement of atoms.

Macromolecules of Cells

Macromolecules—carbohydrates, lipids, proteins, and nucleic acids.

Polymers—largest of the macromolecules

Monomers—small molecule that is a subunit of a polymer. Ex: glucose is a monomer of starch

Macromolecules of Cells

Dehydration reaction—chemical reaction resulting in a covalent bond with accompanying loss of a water molecule.

Hydrolysis reaction—splitting of a compound by the addition of water, with the H+ being incorporated in one fragment and the OH- in the other.

Enzymes—a molecule that speeds a reaction by bringing the reactants together causing the reaction to occur.

Carbohydrates

Carbohydrates used for: Energy Energy storage Structure

Classes of carbohydrates: Monosaccharides Disaccharides ploysaccharides

Monosaccharides

Monosaccharides—consist of only a single sugar molcule or a simple sugar.

Building block of a carbohydrate.

Monosaccharides

Composition of monosaccharides consist of carbon, hydrogen, and oxygen. Simple sugar can have a carbon

backbone of 3-7 Carbons. Named according to number of carbon

atoms▪ Most common: ▪ hexose sugar—glucose

Contains 6 carbon atoms.▪ Pentose sugars—ribose and deoxyribose

Contains 5 carbon atoms

Disaccharides

Disaccharides—two monosaccharides that have joined during a dehydration reaction.

Polysaccharides

Polysaccharides—more than two monosaccharides linked together.

Characteristics: Short-term energy storage molecules. Cannot easily pass through the plasma

membrane, because they are not soluble in water.

Polysaccharides Plant cells store glucose as starch.

Starch can exists in two forms:▪ Non-branched▪ Branched

Animal cells store glucose as glycogen. The storage and release of glucose from liver

cells is under the control of hormones. After we eat, the release of the hormone insulin

from the pancreas promotes the storage of glucose as glycogen.

Polysaccharides as Structural Molecules Some polysaccharides function as

structural components of cells.

Cellulose is the most abundant of all the carbohydrates. Cellulose has long glucose chains that are

held parallel to each other by hydrogen bonding to form microfibrils and then fibers.▪ The fibers crisscross within the plant cell walls for

even more strength.

Polysaccharides as Structural Molecules Chitin is found in the exoskeleton of

crabs and related animals, such as lobsters and insects, is also a polymer of glucose. Chitin is not digestible by humans.

Lipids

Lipid—class of organic compounds that tends to be soluble in nonpolar solvents.

Utilized for both insulation and long-term energy storage by animals. Fat below the skin of marine mammals is

called blubber. Plants use oil instead of fat for long-

term energy storage.

Triglycerides: Long-term Energy Storage Fats and oils contain two types of

unit molecules: glycerol and fatty acids.

Building blocks of lipids are glycerol and fatty acids.

Glycerol is a compound with three hydroxide (OH) groups. OH groups are polar = glycerol is soluble

in water.

Triglycerides: Long-term Energy Storage Fatty acids consist of a long

hydrocarbon chain with a COOH (carboxyl) group at one end.

Fatty acids are either saturated or unsaturated. Saturated fatty acids have no double bonds

between the carbon atoms (fats). Unsaturated fatty acids have double bonds

in the carbon chain (oils).

Triglycerides: Long-term Energy Storage Nearly all animals use fat in

preference to glycogen for long-term energy storage.

Gram per gram, fat stores more energy than glycogen. C—H bonds of fatty acids make them a

richer source of chemical energy than glycogen, because glycogen has several C—OH bonds.

Phospholipids

Phospholipids contain a phosphate group Constructed like a fat, except that in

place of the third fatty acid attached to glycerol, there is a polar phosphate group.▪ The phosphate group is usually bonded to

another organic group, indicated by R.▪ This portion of the molecule becomes the polar head,

while the hydrocarbon chains of the fatty acids become the nonpolar tails.

Phospholipids

Steroids: Four Fused Rings Steroids—are lipids that have

entirely different structures from those of fats.

Skeletons of four fused carbon rings. Each skeleton differs based on the type

functional group attached to the carbon skeleton.

Steroids

Cholesterol is a component of an animal cell’s plasma membrane, and is a precursor of several other steroids.

A diet high in saturated fats and cholesterol can lead to circulatory disorders. The fatty material accumulates inside

the lining of blood vessels, and reduces blood flow.

Waxes

Waxes—long-chained fatty acids bond with long-chain alcohols.

Waxes are solid at normal temperatures because they have high melting points.

Waxes are hydrophobic, resulting in them being waterproof and resistant to degradation.

Waxes

In plants Form a protective cuticle that slows the

loss of water for all exposed parts.

In animals Waxes are involved in skin and fur

maintenance. Earwax contains an organic compound

that at the very least repels insects, and in some cases even kills them.

Proteins

Building Blocks—Amino Acids

Amino Acids: Subunits of Proteins Amino acid—organic molecule

composed of an amino group (NH2), an acid group (COOH), and a R (side group—differs for each of the 20 different kinds of amino acids). Covalent bonds to produce peptide

molecule.

Peptides

Peptide—two or more amino acids bonded together.

Peptide bond—covalent bond between two amino acids.

Dipeptide—two amino acids linked together by a peptide bond.

Polypeptides—three or more amino acids linked together.

Proteins Functions

Support Some proteins make up hair, nails, and

collagen.▪ Lend support to ligaments, tendons, and skin

Enzymes Enzymes bring reactants together and

speed up chemical reactions in cells. They are specific for one particular type

of reaction and can function at body temperature.

Proteins

Transport Channel and carrier proteins in the

plasma membrane allow substances to enter and exit cells.

Some other proteins transport molecules in the blood of animals.▪ Hemoglobin is a complex protein that

transports oxygen.

Proteins

Defense Antibodies are proteins.▪ They combine with foreign substances called

antigens.▪ Prevents antigens from destroying cells and

upsetting homeostasis.

Proteins

Hormones Hormones are regulatory proteins.▪ Serve as intercellular messengers that

influence the metabolism of cells.▪ The hormone insulin regulates the content of

glucose in the blood and in cells.▪ The presence of growth hormone determines the

height of an individual.

Proteins

Motion The contractile proteins actin and

myosin allow parts of cells to move and cause muscles to contract.

Shape of Proteins

The final shape of a protein determines its function in the cells and body of an organism.

A protein can have up to four levels of structure, but not all proteins have all four levels.

Primary Structure

One protein is its own particular sequence of amino acids.

Primary structure is determined by code within nucleic acid molecules.

The level of structure is determined by the sequence of amino acids that join to form polypeptide.

Secondary Structure

Occurs when the polypeptide coils or folds in a particular way.

Linus Pauling and Robert Corey, who began studying the structure of amino acids in the late 1930s, concluded the coiling they called an alpha helix and a pleated sheet the beta sheet.

Secondary Structure

Hydrogen bonds often holds the secondary structure of a polypeptide in place.

Fibrous proteins—structural proteins that exist as helices or pleated sheets that hydrogen-bond to each other.

Tertiary Structure

The tertiary structure is a folding and twisting that results in the final three-dimensional shape of a polypeptide called globular proteins. Then to ball up into rounded shapes.

Enzymes are globular proteins. Each enzyme works best at a specific

temperature and pH.▪ When the protein loses its natural shape its

called denatured.▪ If the shape of the protein changed they cannot work

like they are suppose to in the chemical reaction.

Quaternary Structure

Quaternary structure of a protein consists of more than one polypeptide.

Hemoglobin is a globular protein that consists of four polypeptides.

Nucleic Acids

Nucleic acids—polymers of nucleotides with very specific functions in cells.

Building blocks—nucleotides.

Composition of nucleotides—pentose sugar (ribose or dexoyribose), phosphate, and organic base. Organic bases—adenine, thymine, cytosine,

and guanine or uracil.

DNA

DNA—deoxyribonucleic acid double stranded helix with sugars and

phosphates forming backbone and bases paired in complementary fashion forming “rungs of ladder”.

Function—genetic material that stores information regarding its own replication and the order in which amino acids are to be joined to make a protein.

RNA

RNA—Ribose nucleic acid Single stranded 3 types—▪ ribosomal (rRNA)▪ transfer (tRNA)▪ messenger (mRNA)

DNA

Made of four nucleotides A,T,G,C

Double-stranded Permanent Contains all genes Information, or code,

found in nucleotide sequence (order)

RNA

Made of four nucleotides A,U,G,C

Single-stranded Temporary Copies of gene Information, or code,

found in nucleotide sequence (order)

Structure of DNA and RNA Complementary base pairing—

hydrogen bonding between particular purines and pyrimidines in DNA. The number of purine and pyrimidines in

DNA, regardless or order, are always equal.

Purine bases—adenine (A) and guanine (G)

Pyrimidine bases—cytosine (C) and thymine (T).

Adenosine Triphosphate (ATP) Adenosine composed of adenine and

ribose.

Triphosphate stands for the three phosphate groups that are attached together and to ribose (pentose sugar).

ATP—high-energy molecule because the last two phosphate bonds are unstable and are easily broken.

Adenosine Triphosphate (ATP) When ATP is broken down the energy

released is used by cells for synthesis of macromolecules like carbohydrates and proteins. In muscle cells, the energy is used for

muscle contraction.

ATP is considered the energy currency of cells.

Adenosine Diphosphate (ADP) ATP breaks down to ADP + P

(hydrolysis reaction). Releases energy▪ Used for all the metabolic work done in a cell.

Question

1. Which of these is not a characteristic of carbon? A. forms four covalent bonds B. bonds with other carbon atoms C. is sometimes ionic D. can form long chains E. sometimes shares two pairs of

electrons with another atom

Question

2. The functional group –COOH is… A. acidic B. basic C. never ionized. D. found only in nucleotides E. All of these are correct

Question

3. A hydrophilic group is… A. attracted to water. B. a polar and/or ionized group. C. found at the end of fatty acids. D. the opposite of a hydrophobic group. E. All of these are correct.

Question

4. Which of these makes cellulose nondisgestible in humans? A. a polymer of glucose subunits B. a fibrous protein C. the linkage between the glucose

molecules. D. the peptide linkage between the

amino acid molecules. E. the carboxyl groups ionize.

Question

5. A fatty acid is unsaturated if it… A. contains hydrogen. B. contains carbon—carbon double

bonds. C. contains an acidic group. D. bonds to glycogen. E. bonds to a nucleotide.

Question

6. Which of these is not a lipid? A. steroid B. fat C. polysaccharide D. wax E. phospholipid

Question

7. The difference between one amino acid and another found in the A. amino group B. carboxyl group C. R group D. peptide bond E. carbon atoms

Question

8. ATP A. is an amino acid B. has a helical structure. C. is a high-energy molecule that can

break down to ADP and a phosphate. D. is most energetic when in the ADP

state.

Question

9. The characteristic globular shape of a protein is the A. primary structure B. secondary structure C. Tertiary structure D. Quaternary structure

Question

10. Nucleotide A. contain a sugar, a nitrogen-containing

base, and a phosphate molecule. B. are the monomers for fats and

polysaccharides. C. join together by covalent bonding

between the bases. D. are found in DNA, RNA, and proteins.