3 Proteins, Carbohydrates, and Lipids. 3 Proteins, Carbohydrates, and Lipids 3.1 What Kinds of Molecules Characterize Living Things? 3.2 What Are the

3Proteins, Carbohydrates,

and Lipids

3 Proteins, Carbohydrates, and Lipids

3.1 What Kinds of Molecules Characterize Living Things?

3.2 What Are the Chemical Structures and Functions of Proteins?

3.3 What Are the Chemical Structures and Functions of Carbohydrates?

3.4 What Are the Chemical Structures and Functions of Lipids?

3 Proteins, Carbohydrates, and Lipids

Spider silk is composed of proteins. The protein molecules in different types of silk have different structural characteristics and functions.

Opening Question:

Can knowledge of spider web protein structure be put to practical use?


Molecules that make up living organisms:

• Proteins

• Carbohydrates

• Lipids

• Nucleic acids

Most are polymers of smaller molecules called monomers.


Proteins: combinations of 20 amino acids.

Carbohydrates: sugar monomers (monosaccharides) are linked to form polysaccharides.

Nucleic acids: four kinds of nucleotide monomers.

Lipids: noncovalent forces maintain interactions between lipid monomers.


Macromolecules: polymers with molecular weights >1,000.

Macromolecule function depends on the properties of functional groups— groups of atoms with specific chemical properties and consistent behavior.

A single macromolecule may contain many different functional groups.

Figure 3.1 Some Functional Groups Important to Living Systems (Part 1)




Isomers: molecules with the same chemical formula, but atoms are arranged differently.

• Structural isomers

• cis-trans isomers

• Optical isomers


Structural isomers: differ in how their atoms are joined together.


cis-trans isomers: different orientation around a double bond.


Optical isomers occur when a carbon atom has four different atoms or groups attached to it (an asymmetric carbon).

Some biochemical molecules that can interact with one optical isomer are unable to “fit” the other isomer.

Figure 3.2 Isomers (Part 2)


Biochemical unity: the four kinds of macromolecules are present in the same proportions in all living organisms and have similar functions.

Organisms can obtain required macromolecules by eating other organisms.

Figure 3.3 Substances Found in Living Tissues


Macromolecule functions are directly related to their three-dimensional shapes and the sequence and chemical properties of the monomers.


Polymers are formed in condensation reactions.

Monomers are joined by covalent bonds; energy must be added.

A water is removed; they are also called dehydration reactions.


Polymers are broken down into monomers in hydrolysis reactions (hydro, “water”; lysis, “break”).

Hydrolysis releases energy.

Figure 3.4 Condensation and Hydrolysis of Polymers


Proteins have diverse functions. Only energy storage and information storage are not performed by proteins.

Table 3.1


Proteins are polymers of 20 different amino acids.

Polypeptide chain: single, unbranched chain of amino acids.

Proteins consist of one or more polypeptide chains, which are folded into specific 3-D shapes defined by the sequence of amino acids.


Amino acids have carboxyl and amino groups—they function as both acid and base.

IN-TEXT art, p. 5


The α carbon atom is asymmetrical.

Amino acids exist in two isomeric forms:

D-amino acids (dextro, right)

L-amino acids (levo, left)—this form is found in organisms


The side chains or R-groups also have functional groups.

Amino acids can be grouped based on the side chains.


These hydrophilic amino acids attract ions of opposite charges.

Table 3.2 (Part 2)


Hydrophilic amino acids with polar but uncharged side chains form hydrogen bonds.


Hydrophobic amino acids

Table 3.2 The Twenty Amino Acids (Part C)


The terminal —SH group of cysteine can react with another cysteine side chain to form a disulfide bridge, or disulfide bond (—S—S—).

These are important in protein folding.

Figure 3.5 A Disulfide Bridge


Glycine is small and fits into tight corners in the interior of proteins.

The proline side chain forms a ring, which limits its hydrogen-bonding ability and its ability to rotate about the α carbon. It is often found where a protein bends or loops.


Amino acids bond together covalently in a condensation reaction by peptide linkages (peptide bonds).

Figure 3.6 Formation of Peptide Linkages


A polypeptide chain is like a sentence:

• The “capital letter” is the amino group of the first amino acid—the N terminus.

• The “period” is the carboxyl group of the last amino acid—the C terminus.


The primary structure of a protein is the sequence of amino acids.

The sequence determines secondary and tertiary structure—how the protein is folded.

The number of different proteins that can be made from 20 amino acids is enormous!

Figure 3.7 The Four Levels of Protein Structure (Part 1)


Secondary structure:

• α helix—right-handed coil resulting from hydrogen bonding between N–H groups on one amino acid and C=O groups on another.

• β pleated sheet—two or more polypeptide chains are aligned; hydrogen bonds form between the chains.

Figure 3.7 The Four Levels of Protein Structure (Part 2)

Figure 3.8 Left- and Right-Handed Helices


Tertiary structure: Bending and folding results in a macromolecule with specific three-dimensional shape.

The outer surfaces present functional groups that can interact with other molecules.

Figure 3.7 The Four Levels of Protein Structure (D)


Tertiary structure is determined by interactions between R-groups:

• Disulfide bridges

• Hydrogen bonds

• Aggregation of hydrophobic side chains

• Ionic attractions


Ionic attractions form salt bridges between positively and negatively charged amino acids.

Figure 3.9 Three Representations of Lysozyme

Figure 3.9 Three Representations of Lysozyme

Complete descriptions of tertiary structure have been worked out for many proteins.


If a protein is heated, secondary and tertiary structure break down; the protein is said to be denatured.

When cooled, the protein returns to normal tertiary structure, demonstrating that the information to specify protein shape is in the primary structure.

Figure 3.10 Primary Structure Specifies Tertiary Structure (Part 1)

Figure 3.10 Primary Structure Specifies Tertiary Structure (Part 2)

Working with Data 3.1: Primary Structure Specifies Tertiary Structure

The second protein whose structure was determined was the enzyme ribonuclease A (RNase A).

RNase A has 124 amino acids, including eight cysteines that form four disulfide bridges.


1. The disulfide bonds were destroyed chemically, then allowed to reform.

Protein function was assessed by enzyme activity.

Working with Data 3.1, Figure A


At what time did disulfide bonds begin to form?

At what time did enzyme activity begin to appear?

Explain the difference between these times.


2. Three-dimensional structure was determined by UV spectroscopy. Absorbance of UV over a range of wavelengths was measured.

Working with Data 3.1, Figure B


What are the differences between the peak absorbances of native (untreated) and reduced (denatured) RNase A?

What happened when reduced RNase A was reoxidized (renatured)?

What can you conclude about the structure of RNase A from these experiments?


Quaternary structure results from the interaction of subunits by hydrophobic interactions, van der Waals forces, ionic attractions, and hydrogen bonds.

Each subunit has its own unique tertiary structure.

Figure 3.7 The Four Levels of Protein Structure (E)

Figure 3.11 Quaternary Structure of a Protein


Proteins bind noncovalently with specific molecules. Specificity is determined by:

• Shape—there must be a general “fit” between the 3-D shapes of the protein and the other molecule.

• Chemistry—R groups on the surface interact with other molecules via ionic, hydrophobic, or hydrogen bonds.

Figure 3.12 Noncovalent Interactions between Proteins and Other Molecules


Conditions that affect secondary and tertiary structure:

• High temperature

• pH changes

• High concentrations of polar molecules

• Nonpolar substances


Protein shape can change as a result of:

• Interaction with other molecules— e.g., an enzyme changes shape when it comes into contact with a reactant.

• Covalent modification—addition of a chemical group to an amino acid.

Figure 3.13 Protein Structure Can Change


Proteins can bind to the wrong molecules after denaturation or when they are newly made and still unfolded.

Chaperones are proteins that help prevent this.

Chaperones, such as heat shock proteins, surround a denatured protein and allow it to refold.

Figure 3.14 Molecular Chaperones Protect Proteins from Inappropriate Binding


Carbohydrates have the general formula CmH2nOn. They are:

• sources of stored energy

• used to transport stored energy

• carbon skeletons for many other molecules


Monosaccharides: simple sugars.

Disaccharides: two simple sugars linked by covalent bonds.

Oligosaccharides: 3 to 20 monosaccharides.

Polysaccharides: hundreds or thousands of monosaccharides—e.g., starch, glycogen, cellulose.


All cells use glucose (monosaccharide) as an energy source.

Exists as a straight chain or ring form. Ring is more common—it is more stable.

Ring form exists as α- or β-glucose, which can interconvert.

Figure 3.15 From One Form of Glucose to the Other


Monosaccharides have different numbers of carbons:

Hexoses: six carbons—structural isomers.

Pentoses: five carbons.

Figure 3.16 Monosaccharides Are Simple Sugars


Monosaccharides bind together in condensation reactions to form glycosidic linkages.

Glycosidic linkages can be α or β.

Figure 3.17 Disaccharides Form by Glycosidic Linkages (Part 1)




Oligosaccharides may include other functional groups.

Often covalently bonded to proteins and lipids on cell surfaces and act as recognition signals.

Human blood groups get specificity from oligosaccharide chains.


Polysaccharides are giant polymers of monosaccharides.

Starch: storage of glucose in plants.

Glycogen: storage of glucose in animals.

Cellulose: very stable, good for structural components.

Figure 3.18 Representative Polysaccharides (Part 1)


Carbohydrates can be modified by the addition of functional groups:

• Sugar phosphates

• Amino sugars

• Chitin

Figure 3.19 Chemically Modified Carbohydrates (Part 1)




Lipids are nonpolar hydrocarbons; insoluble in water.

If close together, weak but additive van der Waals forces hold them together.

Not polymers in the strict sense because they are not covalently bonded.


Fats and oils store energy.

Phospholipids—structural role in cell membranes.

Carotenoids and chlorophylls—capture light energy in plants.

Steroids and modified fatty acids—hormones and vitamins.


Animal fat—thermal insulation.

Lipid coating around nerves provides electrical insulation.

Oil and wax on skin, fur, and feathers repels water.


Fats and oils are triglycerides: three fatty acids plus glycerol.

Glycerol: has three –OH groups (an alcohol).

Fatty acid: nonpolar hydrocarbon with a polar carboxyl group.

Carboxyls bond with hydroxyls of glycerol in an ester linkage.

Figure 3.20 Synthesis of a Triglyceride


Saturated fatty acid: no double bonds between carbons—it is saturated with H atoms.

Unsaturated fatty acid: one or more double bonds in carbon chain.

Figure 3.21 Saturated and Unsaturated Fatty Acids


Animal fats tend to be saturated: packed together tightly; solid at room temperature.

Plant oils tend to be unsaturated: the “kinks” prevent packing; liquid at room temperature.

In-Text Art, Ch. 3, p. 57


Fatty acids are amphipathic: they have opposing chemical properties.

When the carboxyl group ionizes it forms COO– and is strongly hydrophilic; the other end is hydrophobic.


Phospholipids: fatty acids bound to glycerol; a phosphate group replaces one fatty acid.

• The “head” is a phosphate group— hydrophilic

• “Tails” are fatty acid chains—hydrophobic

• They are amphipathic

Figure 3.22 Phospholipids (Part 1)


In water, phospholipids line up with the hydrophobic “tails” together and the phosphate “heads” facing outward, forming a bilayer.

Biological membranes have this kind of phospholipid bilayer structure.

Figure 3.22 Phospholipids (Part 2)


Carotenoids: light-absorbing pigments

In-text art p. 20, (-carotene and vitamin A)


Steroids: multiple rings share carbons.

Cholesterol is important steroid in membranes; other steroids function as hormones.


Vitamins—small molecules not synthesized by the body; must be acquired in the diet.

Waxes—highly nonpolar and impermeable to water.

3 Answer to Opening Question

Spider silk is very strong and is used in applications ranging from surgical sutures to bulletproof vests.

Silkworms and bacteria have been genetically engineered to produce spider silk proteins.

The silk is synthesized and stored as a liquid precursor solution, then “spun” out into fibers.

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3 Proteins, Carbohydrates, and Lipids. 3 Proteins, Carbohydrates, and Lipids 3.1 What Kinds of Molecules Characterize Living Things? 3.2 What Are the