Lecture Notes of Biochemistry Chapter 1 (Ref. 2) PDF

Lecture Notes of Biochemistry Chapter 1 (Ref. 2) Biochemistry and the Organization of Cells By Dr. Da'san M. M. Jaradat Al-Balqa Applied University Faculty of Science Department of Chemistry...

Lecture Notes of Biochemistry Chapter 1 (Ref. 2) Biochemistry and the Organization of Cells By Dr. Da'san M. M. Jaradat Al-Balqa Applied University Faculty of Science Department of Chemistry 2021 1  1.1 Basic Themes Biology includes biochemistry, ecology, cell biology, genetics, microbiology, evolutionary theory, botany, zoology, and physiology. Biochemistry is the study of the chemistry of life. Ecology is the study of how organisms interact with each other and with their environment. Cell biology is the study of life on cellular level. Genetics is the study of how organisms pass traits to their offspring. Microbiology is the study of microscopic organisms. Evolutionary theory is the study of changes in types of organism overtime. Botany is study of plants. Zoology is the study of animals. 2 Physiology is the study of the human body.  1.1 Basic Themes Properties of life: 1- Cellular organization 2- Homeostasis: the maintenance of stable internal conditions in spite of changes in external environment. 3- Metabolism. 4- Responsiveness to external environment. 5- Reproduction. 6- Heredity. 7- Growth. 3  1.1 Basic Themes A tissue: is a distinct (‫ )متميز‬group of cells that have similar structures and functions. Examples: bone tissue, lung tissue, leaf tissue (in plants). An organ: is a group of different tissues that are arranged into specialized structure that has a specific function. Examples: bone, lung, leaf (in plants). 4 An organ system: is composed of various organs that carry out a major body function. Examples: circulatory system (‫دوران‬ ‫)جهاز‬ includes heart, blood, and blood vessels. In plants, shoot system (‫ )المجموع الخضري‬consists of stems (‫)الساق‬, leaves, and vascular tissues (‫الوعائية‬ ‫)االنسجة‬. Root system (‫)المجموع الجذري‬. 5  1.2 Chemical Foundations of Biochemistry Organic chemistry is the study of compounds of carbon and hydrogen and their derivatives. Because the cellular apparatus of living organisms is made up of carbon compounds, biomolecules are part of the subject matter of organic chemistry. Additionally, many carbon compounds are not found in any organism, and many topics of importance to organic chemistry have little connection with living things. We are going to concentrate on the aspects of organic chemistry that we need to understand what goes on in living cells. Biomolecules are frequently made up of only six elements—carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus. Central to these biomolecules is carbon, which has the unique property of being able to bond to itself in long chains. 6  1.2 Chemical Foundations of Biochemistry Can a chemist make the molecules of life in a laboratory? The answer is yes. Any compound that occurs in a living organism can be synthesized in the laboratory, although in many cases the synthesis represents a considerable challenge to even the most skilled organic chemist. The reactions of molecules are based on the reactions of their respective functional groups. What makes biomolecules special? Table 1.1 lists some biologically important functional groups. Note that most of these functional groups contain oxygen and nitrogen, which are among the most electronegative elements. As a result, many of these functional groups are polar, and their polar nature plays a crucial role in their reactivity. 7  1.2 Chemical Foundations of Biochemistry Some groups that are vitally important to organic chemists are missing from the table because molecules containing these groups, such as alkyl halides and acyl chlorides, do not have any particular applicability in biochemistry. Conversely carbon-containing derivatives of phosphoric acid are mentioned infrequently in beginning courses on organic chemistry, but esters and anhydrides of phosphoric acid (Figure 1.2) are of vital importance in biochemistry. Adenosine triphosphate (ATP), a molecule that is the energy currency of the cell, contains both ester and anhydride linkages involving phosphoric acid. Important classes of biomolecules have characteristic functional groups that determine their reactions. We shall discuss the reactions of the functional groups when we consider the compounds in which they occur. 8 9 10  1.3 The Beginnings of Biology: Origin of Life Many questions have been raised about the origin of life, such as: - How and when did the Earth come to be? Currently, the most widely accepted cosmological theory for the origin of the Universe is the big bang, a cataclysmic explosion. - How were biomolecules likely to have formed on the early Earth? The atmospheric conditions of the early Earth allowed the formation of molecules, such as amino acids, that play a role in life processes. Experiments have been performed in which the simple compounds of the early atmosphere were allowed to react under the varied sets of conditions that might have been present on the early Earth. The results of such experiments indicate that these simple compounds react abiotically or, as the word indicates (a, “not,” and bios, “life”), in the absence of life, to give rise to biologically important compounds such as the components of proteins and nucleic acids. Of historic interest is the well-known Miller–Urey experiment, shown schematically in Figure 1.4. 11  1.3 The Beginnings of Biology: Origin of Life - How were biomolecules likely to have formed on the early Earth? 12  1.3 The Beginnings of Biology: Origin of Life - How were biomolecules likely to have formed on the early Earth? 13  1.3 The Beginnings of Biology: Origin of Life - How were biomolecules likely to have formed on the early Earth? 14  1.3 The Beginnings of Biology: Origin of Life - Which came first—the catalysts or the hereditary molecules? Several theories describe the origin of living cells from component molecules. All require explanations for coding and for catalytic activity, and all assign an important role to RNA. 15 1.4 The Biggest Biological Distinction— Prokaryotes and Eukaryotes All cells contain DNA. The total DNA of a cell is called the genome. Individual units of heredity, controlling individual traits by coding for a functional protein or RNA, are genes. The types of organisms living today that probably most resemble the earliest cells are the prokaryotes. This word, of Greek derivation (karyon, “kernel, nut”), literally means “before the nucleus.” Prokaryotes include bacteria and cyanobacteria. Prokaryotes are single-celled organisms, but groups of them can exist in association, forming colonies with some differentiation of cellular functions. The word eukaryote means “true nucleus.” Eukaryotes are more complex organisms and can be multicellular or single-celled. 16 1.4 The Biggest Biological Distinction— Prokaryotes and Eukaryotes 17  1.5 Prokaryotic Cells Prokaryotic bacterial cell has a cell wall, which is made up mostly of polysaccharide material, a feature it shares with eukaryotic plant cells. The chemical natures of prokaryotic and eukaryotic cell walls differ somewhat, but a common feature is that the polymerization of sugars produces the polysaccharides found in both. Because the cell wall is made up of rigid material, it presumably serves as protection for the cell. Prokaryotes have a nuclear region, which contains DNA, and ribosome, the site of protein synthesis, as their main features. They have a cell membrane, but do not have an internal membrane system. 18  1.6 Eukaryotic Cells Three of the most important organelles in eukaryotic cells are the nucleus, the mitochondrion, and the chloroplast. Each is separated from the rest of the cell by a double membrane. The nucleus contains most of the DNA of the cell and is the site of RNA synthesis. The mitochondria contain enzymes that catalyze important energy-yielding reactions. Chloroplasts, which are found in green plants and green algae, are the sites of photosynthesis. Both mitochondria and chloroplasts contain DNA that differs from that found in the nucleus, and both carry out transcription and protein synthesis distinct from that directed by the nucleus. Other organelles play specific roles. They include the Golgi apparatus, lysosomes, and peroxisomes. 19 20  1.7 Five Kingdoms, Three Domains In the five-kingdom classification scheme, prokaryotes have a kingdom to themselves (Monera ‫)البدائيات‬. The remaining four kingdoms— plants, animals, protists (‫)الطالئعيات‬, and fungi (‫)الفطريات‬,—consist of eukaryotes. In the three-domain classification schemes, eukaryotes have a domain to themselves. Two domains consist of prokaryotes. Eubacteria are the commonly encountered prokaryotes. Archaea are organisms that live in extreme environments such as those that were found on the early Earth (Extremophiles). 1.8 Common Ground for All Cells Many theories about the rise of eukaryotes from prokaryotes focus on a possible role for symbiosis (‫)التكافل‬. The idea of endosymbiosis, in which a larger cell engulfs a smaller one, plays a large role in scenarios for the development of organelles in eukaryotic cells. 21  1.9 Biochemical Energetics - The Sun is the source of energy for all life on Earth. It provides the energy for photosynthesis, which produces carbohydrates as well as oxygen. Carbohydrates can be processed in chemical reactions that release energy. - Reactions that release energy are favored and thus are likely to occur. Thermodynamics is the branch of science that predicts the likelihood of reactions. 1.10 Energy and Change A spontaneous reaction is one that will take place without outside intervention. This point does not specify reaction rate. Spontaneous does not mean “fast”; some spontaneous processes can take a long time to occur. 22  1.11 Spontaneity in Biochemical Reactions The change in Gibbs free energy (∆G) that accompanies a reaction determines whether that reaction is spontaneous at a given temperature and pressure. ∆G = ∆H-T∆S A negative free energy change (∆G < 0) is characteristic of a spontaneous reaction and the reaction is exergonic (energy released). A positive free energy change (∆G > 0) indicates that the reaction is not spontaneous, but the reverse process is spontaneous and the reaction is endergonic (energy required). When the free energy change is zero (∆G = 0), the reaction is at equilibrium. In any spontaneous process, the entropy of the Universe increases (∆Suniv > 0). 23 24