Chapter 1 Biochemistry and the Organization of Cells

1.1 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

Levels of Structural Organization in the Human Body

1.2 Chemical Foundations of Biochemistry Functional group: an atom or group of atoms that show characteristic physical and chemical properties

ATP and the Reactions for its Formation

1.3 The beginnings of Biology : 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

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

Monomer Polymer

Informational Macromolecules

Biomolecules (Cont’d) 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 (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.11) 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

1.4 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

1.5 Prokaryotes

1.6 Eukaryotic cells A Comparison of a typical animal cell, plant cell, and prokaryotic cell

Fig. 1-14, p. 18

Fig. 1-15, p. 18

Fig. 1-16, p. 19

Fig. 1-17, p. 19

Fig. 1-18, p. 20

Fig. 1-19, p. 20

Fig. 1-19a, p. 20

Fig. 1-19b, p. 20

Table 1-4, p. 21

1.9 Biochemical energries • 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

1.10 Energy and Change

1.11 Spontaneity in biochemical reactions • Life and Thermodynamics G = H - TS 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 • Free Energy of a System G < 0 spontaneous exergonic- energy released G = 0 Equilibrium G > 0 Nonspontaneous endergonic- energy required

Homework Table 1.1 (4 p) Figure 1.6 (10 p) Figure 1.13 (16 p) Table 1.4 (p 21) Review exercises 4, 6, 20, 22, 25