Mary K. Campbell Shawn O.

Farrell
http://academic.cengage.com/chemistry/campbell

Chapter One Biochemistry and the Organization of Cells

Paul D. Adams University of Arkansas

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: 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 Whler in 1828

Levels of Structural Organization in the Human Body

Biomolecules (Contd)
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 (Contd)
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 earths oceans on the surface of clay particles

Biomolecules (Contd)
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 (Contd)
Enzymes: a class of proteins that are biocatalysts
the catalytic effectiveness of a given enzyme depends on its amino acid sequence

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 (Contd)
Which came firstthe 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: 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: Greek derivation meaning before the nucleus
single-celled organisms include bacteria and cyanobacteria

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

Prokaryotes
Cellular Organization
Cell Size Compartmentalization DNA RNA and Protein Cytoplasm Ploidy Cell Replication

Eukaryotes

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

Metabolism

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

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

Important organelles listed in table 1.3

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 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

The energetics of a chemical reaction

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