Che452 Chapter 1

Reginald H. GarrettCharles M. Grisham

www.cengage.com/chemistry/garrett

Reginald Garrett & Charles Grisham • University of Virginia

Chapter 1The Facts of Life:

Chemistry is the Logic of Biological Phenomena

Chapter 1

“…everything that living things do can be understood in terms of the jigglings and wigglings of atoms.”

Richard P. Feynman

Sperm approaching an egg.

Essential Question

• Despite the spectacular diversity of life, the elaborate structure of biological molecules, and the complexity of vital mechanisms, are life functions ultimately interpretable in chemical terms?

Outline and Key Questions

• What Are the Distinctive Properties of Living Systems?

• What Kinds of Molecules Are Biomolecules?• What is the Structural Organization of Complex

Biomolecules?• How Do the Properties of Biomolecules Reflect

Their Fitness to the Living Condition?• What is the Organization and Structure of Cells?• What are Viruses?

On Life and Chemistry…

• “Living things are composed of lifeless molecules.” (Albert Lehninger)

• “Chemistry is the logic of biological phenomena.” (Garrett and Grisham)

1.1 – What Are the Distinctive Properties of Living Systems?

• Organisms are complicated and highly organized

• Biological structures serve functional purposes• Living systems are actively engaged in energy

transformations• Living systems have a remarkable capacity for

self-replication- ultimate test

1.1 – What Are the Distinctive Properties of Living Systems?

Living organisms are complicated and highly organized.

Figure 1.1 (a) Gelada (a baboon); (b) tropical orchid, Ecuador.

1.1 – What Are the Distinctive Properties of Living Systems?

Figure 1.2 The food pyramid. Photosynthetic organisms at the base capture light energy. Herbivores and carnivores derive their energy ultimately from these primary producers.

Solar energy flows from photosynthetic organisms through food chains to herbivores and on to carnivores at the apex of the food pyramid.

Energy-rich moleculesOrganisms capture energy in the form of special energized molecules such as ATP.

Figure 1.3

Energy-rich molecules

Organisms capture energy in the form of special energized molecules such as NADPH.

Figure 1.3

The Fidelity of Self-Replication Resides Ultimately in the Chemical Nature of DNA

Figure 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity.

Covalent Bond Formation by H, C, N, and O Makes Them Suitable to the Chemistry of Life

Figure 1.6 Covalent bond formation by e- pair sharing makes H, C, N, and O appropriate for the support of life.

1.2 What Kinds of Molecules are Biomolecules?

1.2 What Kinds of Molecules are Biomolecules?

• H, O, C and N make up 99+% of atoms in the human body

ELEMENT PERCENTAGE

Hydrogen 63

Oxygen 25.5

Carbon 9.5

Nitrogen 1.4

1.2 What Kinds of Molecules are Biomolecules?

• What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life?

• Answer: Their ability to form covalent bonds by electron-pair sharing.

1.2 What Kinds of Molecules are Biomolecules?

• What are the bond energies of covalent bonds? Bond Energy (kJ/mol)

H-H 436C-H 414C-C 343C-O 351

1.2 What Kinds of Molecules are Biomolecules?

Covalent bond formation by e- pair sharing

1.2 What Kinds of Molecules are Biomolecules?

Covalent bond formation by e- pair sharing

1.3 What is the Structural Organization of Complex Biomolecules?

• Simple Molecules are the Units for Building Complex Structures

– Metabolites and Macromolecules– Organelles– Membranes– The Unit of Life is the Cell

1.3 What is the Structural Organization of Complex Biomolecules?

Examples of the versatility of C-C bonds in building complex structures

1.3 What is the Structural Organization of Complex Biomolecules?

Examples of the versatility of C-C bonds in building complex structures

1.3 What is the Structural Organization of Complex Biomolecules?

Examples of the versatility of C-C bonds in building complex structures

1.3 What is the Structural Organization of Complex Biomolecules?

Examples of the versatility of C-C bonds in building complex structures

1.3 What is the Structural Organization of Complex Biomolecules?

1.3 What is the Structural Organization of Complex Biomolecules?

1.3 What is the Structural Organization of Complex Biomolecules?

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

• Macromolecules and their building blocks have a “sense” or directionality

• Macromolecules are informational• Biomolecules have characteristic three-

dimensional architecture• Weak forces maintain biological structure and

determine biomolecular interactions

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Amino acids build proteins

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Polysaccharides are built by joining sugars together

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Nucleic acids are polymers of nucleotides

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

• Covalent bonds hold atoms together so that molecules are formed

• Weak forces profoundly influence the structures and behaviors of all biological molecules

• Weak forces create interactions that are constantly forming and breaking under physiological conditions

• Energies of weak forces range from 0.4 to 30 kJ/mol• Weak forces include:

– van der Waals interactions– Hydrogen bonds– Ionic interactions– Hydrophobic interactions

Biomolecules Have Characteristic Three-Dimensional Architecture

Figure 1.11 Antigen-binding domain of immunoglobulin G (IgG).

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

• Know these important numbers

• Van der Waals Interactions: 0.4-4.0 kJ/mol• Hydrogen Bonds: 12-30 kJ/mol• Ionic Interactions: 20 kJ/mol• Hydrophobic Interactions: <40 kJ/mol

• These interactions influence profoundly the nature of biological structures

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Two Important Points about Weak Forces

• Biomolecular recognition is mediated by weak chemical forces

• Weak forces restrict organisms to a narrow range of environmental conditions

Van der Waals Forces Are Important to Biomolecular Interactions

Figure 1.12 Van der Waals packing is enhanced in molecules that are structurally complementary. Gln121, a surface protuberance on lysozyme, is recognized by the antigen-binding site of an antibody against lysozyme.

Van der Waals Forces Are Important to Biomolecular Interactions

Figure 1.13 The van der Waals interaction energy profile as a function of the distance, r, between the centers of two atoms.

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Some biologically important H bonds

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Some biologically important H bonds

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Ionic bonds in the Mg-ATP complex

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Ionic bonds contribute to the stability of proteins

Biomolecular Recognition is Mediated by Weak Chemical Forces

Figure 1.16 Structural complementarity: The antigen on the right (gold) is a small protein, lysozyme, from hen egg white. The antibody molecule (IgG) (left) has a pocket that is structurally complementary to a surface feature (red) on the antigen.

Biomolecular Recognition is Mediated by Weak Chemical Forces

Figure 1.16 Structural complementarity: The antigen on the right (gold) is a small protein, lysozyme, from hen egg white. The antibody molecule (IgG) (left) has a pocket that is structurally complementary to a surface feature (red) on the antigen.

Biomolecular Recognition is Mediated by Weak Chemical Forces

Figure 1.16 Puzzles and locks in keys are models of structural complementarity.

Biomolecular Recognition is Mediated by Weak Chemical Forces

Figure 1.17 Denaturation and renaturation of the intricate structure of a protein.

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Cells release the energy of glucose in a stepwise fashion, capturing it in the formation of ATP

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

Combustion of glucose in a calorimeter yields energy in its least useful form, heat

Enzymes Catalyze Metabolic Reactions

Figure 1.19 Carbonic anhydrase, a representative enzyme. Hydration of CO2 (responsibility)

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

The Time Scale of Life:• The processes of life have durations ranging

over 33 orders of magnitude• From 10-15 sec (for electron transfer reactions)• To 1018 sec (the period of evolution, from the

first appearance of organisms to today)• The processes and lifetimes described in Table

1.5 will be discussed throughout the text and course

1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

1.5 What is the Organization and Structure of Cells?

• Prokaryotic cells– A single (plasma) membrane– No nucleus or organelles

• Eukaryotic cells– Much larger in size than prokaryotes– 103-104 times larger!– Nucleus plus many organelles– ER, Golgi, mitochondria, etc.

How Many Genes Does a Cell Need?

Archaea and Bacteria Have a Relatively Simple Structural Organization

Figure 1.20 This bacterium is Escherichia coli, a member of the coliform group of bacteria that colonize the intestinal tract of humans. (See Table 1.7.)

Arcahea and Bacteria Have a Relatively Simple Structural Organization

The Structural Organization of Eukaryotic Cells Is More Complex Than That of Prokaryotic Cells

Figure 1.21 Several images of organelles in eukaryotic cells.

The Structural Organization of Eukaryotic Cells Is More Complex Than That of Prokaryotic Cells

Figure 1.21 This figure diagrams a rat liver cell, a typical higher animal cell.

1.5 What is the Organization and Structure of Cells?

Figure 1.22 Electron micrograph of a chloroplast.

1.5 What is the Organization and Structure of Cells?

Figure 1.22 Electron micrograph of a Golgi body.

1.5 What is the Organization and Structure of Cells?

Figure 1.22 Electron micrograph of a nucleus

1.5 What is the Organization and Structure of Cells?

Figure 1.22 This figure diagrams a cell in the leaf of a higher plant

1.5 What is the Organization and Structure of Cells?

1.5 What is the Organization and Structure of Cells?

1.5 What is the Organization and Structure of Cells?

1.6 What Are Viruses?

Figure 1.23 Viruses are genetic elements enclosed in a protein coat. Viruses are not free-living organisms and can reproduce only within cells. Viruses show an almost absolute specificity for their particular host cells, infecting and multiplying only within those cells. Viruses are known for virtually every kind of cell. Shown here are examples of (a) an animal virus, adenovirus; (b) bacteriophage T4 on E.coli; and (c) a plant virus, tobacco mosaic virus.

1.6 What are Viruses?

Figure 1.24 The virus life cycle. Viruses are mobile bits of genetic information encapsulated in a protein coat.