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Chapter 3

Lecture Outline

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Chapter 3

The Chemical Basis of Life II: Organic Molecules

Key Concepts:

• The Carbon Atom

• Formation of Organic Molecules and Macromolecules

• Overview of the Four Major Classes of Organic Molecules Found in Living Cells

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

The Carbon Atom

• Organic molecules contain carbon

• Organic molecules are abundant in living organisms

• Macromolecules are large, complex organic molecules

Carbon

Carbon has 4 electrons in its outer shell

Needs 4 more electrons to fill the shell

It can make up to four bonds

• Usually single or double bonds

Carbon can form nonpolar or polar bonds

• Molecules with polar bonds are water soluble

• Molecules with nonpolar bonds (like hydrocarbons) are not very water soluble

Figure 3.1

a) Electron orbitals in carbon

b) Simplified depiction of carbon’s electron shells

Figure 3.2

Propionic acid

C—C and C—H bonds are electrically neutral and nonpolar.

Oxygen is more electronegative than carbon; thus, C—O and C=O bonds are polar.

Functional Groups

• Groups of atoms with special chemical features that are functionally important

• Each type of functional group exhibits the same properties in all molecules in which it occurs

Table 3.1 top half

Table 3.1 Some Biologically Important Functional Groups That Bond to Carbon

Functional group* (with shorthand notation) Formula' Examples of where the group is found Properties

Amino (-NH2) Amino acids (proteins) Weakly basic (can accept +

H ); polar; forms part of peptide bonds

Carbonyl (-CO)‡

Ketone Steroids, waxes, and proteins Polar; highly chemically reactive; forms

hydrogen bonds

Aldehyde (-CHO) Linear forms of sugars and some odor molecules

Carboxyl (-COOH) Amino acids, fatty acids Acidic (gives up +H in water); forms part of peptide bonds

Hydroxyl (-OH) Steroids, alcohol, carbohydrates, some amino acids Polar; forms hydrogen bonds with water

*This list contains many of the functional groups that are important in biology. However, many more functional groups have been identified by biochemists. †R and R' represent the remainder of the molecule. ‡A carbonyl group is C=O. In a ketone, the carbon of this group forms covalent bonds with two other carbon atoms. In an aldehyde, the carbon is bonded to a hydrogen atom.

Table 3.1 bottom half

Table 3.1 Some Biologically Important Functional Groups That Bond to Carbon

Functional group* (with shorthand notation) Formula' Examples of where the group is found Properties

Methyl (-CH3) May be attached to DNA, proteins, and carbohydrates

Nonpolar

Phosphate  24PO 

 Nucleic acids, ATP, phospholipids Polar; weakly acidic and negatively charged at typical pH of living organisms

Sulfate  4SΟ 

 May be attached to carbohydrates, proteins, and lipids

Polar; negatively charged at typical pH of living organisms

Sulfhydryl (-SH) Proteins that contain the amino acid cysteine

Polar; forms disulfide bridges in many proteins

Isomers

Two molecules with an identical molecular formula but different structures and characteristics

Structural isomers - contain the same atoms but in different bonding relationships

Stereoisomers - identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers

• Cis-trans isomers - positioning around double bond

• Enantiomers - mirror image molecules

Figure 3.3

a) Structural isomers

b) Two types of stereoisomers

Formation of Organic Molecules

and Macromolecules 1

Condensation reaction

Links monomers to form polymers

A polymer begins as two monomers combine in a dehydration reaction.

Elongation of the polymer continues with additional dehydration reactions.

The final polymer may consist of many monomers.

Formation of Organic Molecules

and Macromolecules 2

Hydrolysis reaction

Polymers broken down into monomers.

Polymer formation by dehydration reactions

A molecule of water is removed each time a new monomer is added, thus a “dehydration” reaction

The process repeats to form long polymers

A polymer can consist of thousands of monomers

Dehydration is catalyzed by enzymes

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Breakdown of a polymer by hydrolysis reactions

• A molecule of water is added back each time a monomer is released

• The process repeats to break down long polymer

• Hydrolysis is catalyzed by enzymes

Carbohydrates

• Composed of carbon, hydrogen, and oxygen atoms

• Cn(H2O)n

• Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group

Monosaccharides Simplest sugars

Most common are 5 or 6 carbons

Pentoses • Ribose C5H10O5 • Deoxyribose (C5H10O4)

Hexose • Glucose (C6H12O6)

Different ways to depict structures

Ring Linear

Figure 3.5a

a) Linear and ring structures of D-glucose

Glucose isomers

Structural isomers

Different arrangement of same elements

Example: Glucose and galactose

Stereoisomers

α andβ glucose‐‐ • Hydroxyl group of carbon 1 is above or below ring

D- and L-glucose • Enantiomers with mirror image structure

Disaccharides

• Composed of two monosaccharides

• Joined by dehydration or condensation reaction

Glycosidic bond

• Broken apart by hydrolysis

• Examples: sucrose, maltose, lactose

Figure 3.5b

b) Isomers of glucose

Figure 3.6

Polysaccharides

• Many monosaccharides linked together to form long polymers

• Examples:

Energy storage – starch, glycogen

Structural – cellulose, chitin, glycosaminoglycans

Figure 3.7

Lipids

• Composed predominantly of hydrogen and carbon atoms

• Defining feature of lipids is that they are nonpolar and therefore very insoluble in water

• Include fats, phospholipids, steroids, waxes

• Lipids comprise about 40% of the organic matter in the average human body

Fats 1

• Also known as triglycerides or triacylglycerols

• Formed by bonding glycerol to 3 fatty acids

• Joined by dehydration; broken apart by hydrolysis

The hydrogens from each hydroxyl group in glycerol are removed.

The hydroxyl groups from each carboxyl group of the 3 fatty acids are removed.

The new bond created is called an ester bond.

Fatty acids

• Saturated – all carbons linked by single bonds Tend to be solid at room temperature

• Unsaturated – contain one or more double bonds Tend to be liquid at room temperature (known as oils)

Cis forms naturally; trans formed artificially

Trans fats are linked to disease

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Figure 3.10

• Animal fats are usually saturated fats

• Plant fats are usually unsaturated fats

a) Animal fats at high and low temperatures

b) Vegetable fats at low temperature

High temperature converts solid, saturated fasts to liquid.

After cooling, saturated fats return to their solid form.

Unsaturated fats have low melting points and are liquid at room temperature.

a (left, right): ©Tom Pantages; b: ©Felicia Martinez Photography/PhotoEdit

Fats 2

• Fats are important for energy storage

1 gram of fat stores more energy than 1 gram of glycogen or starch

• Fats can also be structural, providing cushioning and insulation

Phospholipids • Formed from glycerol, two fatty acids and a

phosphate group

• Phospholipids are amphipathic molecules

Phosphate head – polar / hydrophilic

Fatty acid tail – nonpolar / hydrophobic

Figure 3.11a and b

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Steroids

• Four interconnected rings of carbon atoms

• Usually insoluble in water

• Example: Cholesterol

• Tiny differences in structure can lead to profoundly different, specific biological properties Estrogen versus testosterone

Figure 3.12 1

Figure 3.12 2

(left, right): ©Adam Jones/Science Source

Proteins

• Composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur

• Building blocks of proteins are amino acids

20 different amino acids

Common structure with variable sidechain that determines structure and function

Amino acid structure

General designation for an amino acid side chain

Amino group - positively charged at neutral pH

Carboxyl group - negatively charged at neutral pH

Figure 3.13

Figure 3.13: Nonpolar Amino Acids only

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Figure 3.13 Polar Amino Acids – Uncharged and Charged

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Polypeptide formation

• Amino acids joined by dehydration reaction

Carboxy + amino forms peptide bond

Polymers of amino acids known as polypeptides

Proteins may be formed from one or several polypeptides

• Polypeptides are broken down by hydrolysis

Figure 3.14a: Reactants only

a) Formation of a peptide bond between 2 amino acids

Formation of a peptide bond

Figure 3.14a, b, and c

a) Formation of a peptide bond between 2 amino acids

b) Polypeptide – a linear chain of amino acids

c) Numbering system of amino acids in a polypeptide Access the text alternative for slide images.

Figure 3.15

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Primary structure

• Amino acid sequence

• Encoded directly by genes

Secondary Structure

• Chemical and physical interactions cause protein folding

• α helices and β pleated sheets Key determinants of a protein’s characteristics

• “Random coiled regions” Not α helix or β pleated sheet Shape is specific and important to function

Tertiary structure

• Folding gives protein complex 3D shape

• This is the final level of structure for a single polypeptide chain

Quaternary structure

• Made up of two or more polypeptides

Individual polypeptide chains are protein subunits

Protein can be formed from several copies of the same polypeptide

Or may be multimeric – composed from different polypeptides

Five factors that promote protein folding and stability

• Hydrogen bonds

• Ionic bonds and other polar interactions

• Hydrophobic effects

• Van der Waals forces

• Disulfide bridges

Figure 3.17

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Protein-protein interactions

Many cellular processes involve steps in which two or more different proteins interact

Specific binding at surface

Use first four factors to bind

• Hydrogen bonds

• Ionic bonds and other polar interactions

• Hydrophobic effects

• Van der Waals forces

Figure 3.18

Anfinsen Showed That the Primary Structure of Ribonuclease

Determines Its Three-Dimensional Structure

• Prior to 1960s, the mechanisms by which proteins assume their 3D structures were not understood.

• Christian Anfinsen postulated that proteins contain all the information necessary to fold into their proper conformation without needing organelles or factors

• He hypothesized that proteins spontaneously assume their most stable conformation based on the laws of chemistry and physics

Anfinsen’s Ribonuclease experiment 1

• Won him the Nobel Prize in 1972

• Performed in vitro - no other cellular components present

• Chemicals that disrupt bonds caused the enzyme to lose function; removal of those chemicals restored function

• Conclusion:

Even in the complete absence of any cellular factors or organelles, an unfolded protein can

refold into its functional structure

• Since then, we have learned that some proteins do require assistance in folding

Anfinsen’s Ribonuclease experiment 2

HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, three-dimensional shapes.

KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion chromatography columns.

1. Incubate purified ribonuclease in test tube with RNA, and measure its ability to degrade RNA.

Numerous H bonds and ionic bonds (not shown) and 4 S—S bonds. Protein is properly folded. (For simplicity, the three- dimensional shape is not shown; see Panel 3 for a computer model of the true structure.)

2. Denature ribonuclease by adding β-mercaptoethanol (breaks S—S bonds) and urea (breaks H bonds and ionic bonds). Measure its ability to degrade RNA.

No more H bonds, ionic bonds, or S—S bonds. Protein is unfolded.

Feature investigation HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, three-dimensional shapes.

KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion chromatography columns.

3. Pour mixture from step 2 into a size-exclusion chromatography column. Beads in the column trap β-mercaptoethanol and urea, whereas ribonuclease flows to the bottom. Collect ribonuclease in a test tube. Allow ribonuclease to sit for up to 20 hours and then measure its ability to degrade RNA.

Beads have microscopic pores that trap β-mercaptoethanol and urea, but not ribonuclease.

Computer model of properly folded structure of ribonuclease

4. THE DATA 5. CONCLUSION Certain proteins, like ribonuclease, can spontaneously fold into their final, functional shapes without assistance from other cellular structures or factors. (However, as described in the text, this is not true of many other proteins.)

6. SOURCE Haber, E., and Anfinsen, C.B. 1961. Regeneration of enzyme activity by air oxidation of reduced subtilisin-modified ribonuclease. Journal of Biological Chemistry 236:422 to 424.

Proteins Contain Functional Domains Within Their Structures

• Modules or domains in proteins have distinct structures and function

• Example: Signal transducer and activator of transcription (STAT) protein

• Each domain of this protein is involved in a distinct biological function

• Proteins that share a particular domain also share the associated function

Genomes & Proteomes

Nucleic Acids

Responsible for the storage, expression, and transmission of genetic information

Two classes

Deoxyribonucleic acid (DNA)

• Stores genetic information encoded in the sequence of nucleotide monomers

Ribonucleic acid (RNA)

• Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain

Nucleic acid monomer is a nucleotide

Made up of phosphate group, a five-carbon sugar (either ribose or deoxyribose), and a single or double ring of carbon and nitrogen atoms known as a base

Nucleotides are linked into polymer by a sugar-phosphate backbone

Figure 3.22

DNA versus RNA

DNA RNA

Deoxyribonucleic acid Ribonucleic acid

Deoxyribose Ribose

Thymine (T) Uracil (U)

Adenine (A), guanine (G), cytosine (C) used in

both

Adenine (A), guanine (G), cytosine (C) used in

both

2 strands, double helix Single strand

1 form Several forms

Figure 3.23

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