Paul D. Adams • University of Arkansas

Mary K. CampbellShawn O. Farrellhttp://academic.cengage.com/chemistry/campbell

Chapter One Biochemistry and the Organization of

Cells

Some Basic Themes• All living things make use of the same types of biomolecules, and all

use energy– as a result, all living things can be studied using the methods

of chemistry and physics

• The fundamental similarity of cells of all types makes it interesting to speculate on the origins of life– both cells and the biomolecules of which they are made must

have arisen ultimately from very simple molecules, such as H2O, CH4, CO2, NH3, N2, and H2

• Field of Biochemistry draws many disciplines• allows us to answer questions related to molecular nature of

life

Biomolecules

• Organic chemistry:Organic chemistry: the study of the compounds of carbon– the cellular apparatus of living organisms is made

up of carbon compounds– biomolecules are part of the subject matter of

organic chemistry– the reactions of biomolecules can be described by

the methods of organic chemistry

• The experiment of Friedrich Wöhler in 1828

Levels of Structural Organization in the Human Body

Biomolecules (Cont’d)

• Functional group:Functional group: an atom or group of atoms that shows characteristic physical and chemical properties

ATP and The Reactions for its Formation

Origins of Life• The “big bang” theory

– all matter was originally confined in a very small space– as the result of an explosion, it started to expand with great

force; temperature approx. 15 x 109 K– the average temperature of the universe has been decreasing

ever since– in the earliest stages of the universe, the only elements present

were H, He, and Li– other elements formed by

• thermonuclear reactions in stars• explosions of stars• the action of cosmic rays outside the stars

Relative Abundance of Important Elements

Biomolecules (Cont’d)• Gases present in the atmosphere of the early earth included

NH3, H2S, CO, CO2, CH4, N2, H2, and H2O but not O2

• Experiments have demonstrated that important biomolecules, such as proteins and nucleic acids, could have arisen under abiotic (nonliving) conditions from reactions of these simple compounds– in the earth’s oceans– on the surface of clay particles

Biomolecules (Cont’d)• Living cells include very large molecules, such as proteins,

nucleic acids, polysaccharides, and lipids– these biomolecules are polymers (Greek: poly + meros, many +

parts)– they are derived from monomers (Greek: mono + meros, single

+ part) --amino acids --> proteins --nucleotides --> nucleic acids --monosaccharides --> polysaccharides --glycerol and 3 fatty acids --> lipids

Informational Macromolecules

Biomolecules (Cont’d)

• Enzymes:Enzymes: a class of proteins that are biocatalysts– the catalytic effectiveness of a given enzyme depends on its

amino acid sequence• Genetic code:Genetic code: the relationship between the nucleotide

sequence in nucleic acids and the amino acid sequence in proteins– theories of the origin of life consider how such a coding system

might have arisen

Biomolecules (Cont’d)

• Which came first…the chicken or the egg?• catalytic activity associated with proteins• coding associated with nucleic acids

• It has been discovered recently that certain types of RNA have catalytic activity and are capable of catalyzing their own further processing (See Figure 1.7 p.12)• RNA is now considered by many scientists to have

been the original coding material• it still serves this function in some viruses

The “RNA World”• The appearance of a form of RNA capable of coding for

its own replication was the pivotal point in the origin of life

• This original RNA both encoded for and catalyzed its own replication

• In time, this system evolved to encode for the synthesis of protein catalysts

• Even later, DNA became the primary genetic material, and RNA took on only an intermediary role in the synthesis of proteins

Stages in the Evolution of Self-replicating RNA Molecules

Theories on the Origin of Life• A key point in the development of living cells is the

formation of membranes that separate cells from their environment

• Some theories of the origin of life focus on proteins– according to one model, proteinoids aggregated

to form microspheres• Double-Origin theory:Double-Origin theory: the development of a coding

system and the development of catalysis came about separately– a combination of the two later in time produced

life as we know it.

Prokaryotes and Eukaryotes

•• Prokaryote:Prokaryote: Greek derivation meaning “before the nucleus”

– single-celled organisms– include bacteria and cyanobacteria

•• Eukaryote:Eukaryote: Greek derivation meaning “true nucleus”• contain a well-defined nucleus surrounded by a

nuclear membrane• can be single celled, such as yeasts and

Paramecium, or multicellular, such as animals and plants

Comparison of Prokaryotes and Eukaryotes

Comparison of Prokaryotic and Eukaryotic Cell

mainly unicellular

0.2-5m in diameter anaerobic or aerobic No

free in cytoplasm as nucleoid

RNA & protein synthesized in the same compartment

no cytoskeleton

usually haploid simple division

following DNA replication

mainly multicellular; with differentiation of many cell types

10-50m in diameter aerobic Yes, with several kinds of

organelles in nucleus, condensed with

proteins into chromosomes RNA synthesized in nucleus;

proteins in the cytoplasm cytoskeleton composed of

protein filaments

almost always diploid or polyploid

mitosis in somatic cells; meiosis in gamete formation

Prokaryotes

EukaryotesCellular Organization

Cell Size

Metabolism

Compartmentalization

DNA

RNA and Protein

Cytoplasm

Ploidy

Cell Replication

• Important organelles listed in table 1.3

A Comparison of a typical animal cell, plant cell, and prokaryotic cell

Mitochondria

Site of ATP production via

aerobic metabolism Key Features

outer membrane intermembrane space inner membrane matrix

Chloroplasts Site of photosynthesis in

plants and green algae Key Features

outer membrane intermembrane space inner membrane stroma thylakoid membrane thylakoid lumen

Lysosomes

Responsible for degrading certain cell components material internalized

from the extracellular

environment Key Features

single membrane pH of lumen 5 acid hydrolases carry

out degradation reactions

Peroxisomes

Responsible for degrading

fatty acids toxic compounds

Key Features single membrane contain oxidases and

catalase

Five Kingdoms, Three Domains

• 5-kingdom system takes into account differences between prokaryotes and eukaryotes

• Provides classification for eukaryotes that are neither plants nor animals

• Kingdoms are: Monera, Protista, Fungi, Plantae, and Anamilia

Five Kingdoms, Three Domains

What is source of energy in cells?• Light from the sun is the ultimate source of

energy for all life on earth– photosynthetic organisms use light energy to drive

the energy-requiring synthesis of carbohydrates– non-photosynthetic organisms consume these

carbohydrates and use them as energy sources• The energetics of a chemical reaction

• if the change in free energy is negative (free energy decreases), the reaction is spontaneous as written

• if the change in positive (free energy increases), the reaction will not occur as written unless energy is supplied from an external source

How are energy changes measured?

Thermodynamics- branch of science that answers questions about processes that are energetically favorable

Spontaneity in biochemical reactions

• Free Energy of a System G < 0 spontaneous exergonic- energy released

G= 0 Equilibrium

G > 0 Nonspontaneous endergonic- energy required

• Life and Thermodynamics G=H-TS

H is heat of a reaction at constant pressure

S is the change in entropy

G is the change in free energy

• T is the temperature