UNIT 1 - Biochemistry and The Organization of Cells.pdf

The Legazpi Thomasian Prayer God of all nations, beneficent creator and generous provider, You who guide all creation to its proper perfection, enlighten our vision and guide our mission that we may see clearly and love truly as we realize our goals and...

The Legazpi Thomasian Prayer God of all nations, beneficent creator and generous provider, You who guide all creation to its proper perfection, enlighten our vision and guide our mission that we may see clearly and love truly as we realize our goals and objectives. Imbue us with Your unending grace, that we may flourish as persons integrally, and be one in mind and heart as a community. Keep our passion for the truth bright and our compassion for humanity burning empowering us to be agents of Christian social transformation. The Legazpi Thomasian Prayer Sustain us in harmony with nature that we may be responsible stewards of Your creation. Merciful Lord of our restless being. strengthen us to soar beyond the limits of our weakness and vulnerability, So that we may praise, bless, and preach You in a life of truth and love out of gratitude. We ask this, O Loving Father, through Jesus Christ Your Son, in the unity of the Holy Spirit, God forever and ever. Amen.  UNIT 1: Biochemistry and the Organization of Cells ERIC D. ALINA, LPT Instructor II, CASE University of Santo Tomas-Legazpi  UNIT I OUTLINE 1-1 Basic Themes 1-2 Chemical Foundations of Biochemistry 1-3 The Beginnings of Biology 1-4 The Biggest Biological Distinction – Prokaryotes and Eukaryotes 1-5 How We Classify Eukaryotes and Prokaryotes 1-6 Biochemical Energetics 4 1-1 BASIC THEMES 5  BIOCHEMISTRY AND LIFE How does Biochemistry describe life processes? 1-1 Basic Themes  How does Biochemistry describe life processes? 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. 1-1 Basic Themes  BIOCHEMISTRY AND LIFE How did living things originate? 1-1 Basic Themes  How did living things originate? 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 𝑯𝟐 𝑶, 𝑪𝑯𝟒 , 𝑪𝑶𝟐 , 𝑵𝑯𝟑 , 𝑵𝟐 , 𝒂𝒏𝒅 𝑯𝟐 ▧ the field of biochemistry draws many disciplines ▧ allows us to answer questions related to molecular nature of life processes 1-1 Basic Themes  The MRI (Magnetic Resonance Imaging) 1-1 Basic Themes  Cell = City? 1-1 Basic Themes  Cells = Transportation System? 1-1 Basic Themes “ 13  1-3 CHEMICAL FOUNDATIONS OF BIOCHEMISTRY 14  Organic chemistry is the study of compounds or carbon and hydrogen and their derivatives. Biomolecules are part of the subject matter of organic chemistry. Why? 15 1-2 Chemical Foundations of Biochemistry  AMINO ACIDS It has a central carbon, amino group, carboxyl group, and R group. Under physiological conditions, both carboxyl and amino groups are ionized. 16 1-2 Chemical Foundations of Biochemistry  CARBOHYDRATES It is made up of C, H, and O, with a general formula: 𝐶𝐻2 𝑂 𝑛 Where n is at least 3. 17 1-2 Chemical Foundations of Biochemistry  NUCLEOTIDES It is composed of 5- carbon sugar, a nitrogen-containing ring, and 1 or more phosphate groups 18 1-2 Chemical Foundations of Biochemistry  LIPIDS the most diverse biomolecule; poorly soluble in water. 19 1-2 Chemical Foundations of Biochemistry  LIPIDS the most diverse biomolecule; poorly soluble in water. 20 1-2 Chemical Foundations of Biochemistry Is it possible to make the molecules of life in a laboratory? 21  German chemist Friedrich Wöhler performed the critical experiment disproving “vital forces”. He synthesized urea from ammonium cyanate. 22 1-2 Chemical Foundations of Biochemistry  23 1-2 Chemical Foundations of Biochemistry  Functional Groups Important in Biochemistry 24 1-2 Chemical Foundations of Biochemistry  25 1-2 Chemical Foundations of Biochemistry  26 1-2 Chemical Foundations of Biochemistry  27 1-2 Chemical Foundations of Biochemistry  28 1-2 Chemical Foundations of Biochemistry  29 1-2 Chemical Foundations of Biochemistry 1-3 THE BEGINNINGS OF BIOLOGY  THE EARTH AND ITS AGE How and when did the Earth come to be? 1-3 The Beginnings of Biology  How and when did the Earth come to be? The “Big Bang” theory: 1. All matter was originally confined to a comparatively small volume of space. 2. As the result of explosion, it started to expand with great force; temperature approx. 15 × 109 K. 1-3 The Beginnings of Biology  How and when did the Earth come to be? The “Big Bang” theory: 3. The average temperature of the universe has been decreasing ever since. 4. In the early stages of the universe, the only elements present were H, He, and Li. 5. Other elements are formed by: (a) thermonuclear reactions of stars; (b) explosions of stars; and (c) the action of cosmic rays outside the stars. 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 36  BIOMOLECULES How were biomolecules likely to have formed on the early Earth? 1-3 The Beginnings of Biology  How were biomolecules likely to have formed on the early Earth? The result of experimenting simple compounds of early Earth indicate that these simple compounds react abiotically. The Miller-Urey experiment simulates the conditions of early Earth and the formation of early amino acids. 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology  Living cells include very large molecules, such as proteins, nucleic acids, polysaccharides, and lipids. These biomolecules are polymers, which are derived from monomers. Monomers → Polymers Amino acids → Proteins Nucleotides → Nucleic Acids Monosaccharides → Polysaccharides Glycerol and 3 fatty acids → Lipids 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology  Enzyme: 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 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology  MOLECULES TO CELLS Which came first, the catalysts or the hereditary molecules? 1-3 The Beginnings of Biology  Which came first, the catalysts or the hereditary molecules? Which comes first, chicken or egg? 1-3 The Beginnings of Biology  Two Theories of the Possible Origin of Life 53 1-2 Chemical Foundations of Biochemistry  TWO THEORIES: 1. The RNA-world Theory 2. The Double-Origin Theory 54 1-2 Chemical Foundations of Biochemistry  The RNA-world Theory RNA (ribonucleic acid) is capable of catalyzing its own processing. RNA, rather than DNA, is now considered by many scientists to have been the original coding material, and it still serves this function in some viruses. 1-3 The Beginnings of Biology  The RNA-world Theory The appearance of a form of RNA capable of coding for its own replication was the pivotal point in the origin of life. 1-3 The Beginnings of Biology 56 1-3 The Beginnings of Biology  How did nucleic acid synthesis (which requires many protein enzymes) and protein synthesis (which requires the genetic code to specify the order of amino acids) come to be? 1-3 The Beginnings of Biology 58  The RNA-world Theory (continued) According to this hypothesis, RNA (or a system of related kinds of RNA), originally played both roles, catalyzing and encoding its own replication. 1-3 The Beginnings of Biology 59 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology  The Double-Origin Theory The development of catalysis and the development of a coding system came about separately, and the combination of the two produced life as we know it. The rise of aggregates of molecules capable of catalyzing reactions was one origin of life, and the rise of a nucleic acid-based coding system was another origin. 1-3 The Beginnings of Biology 62 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-3 The Beginnings of Biology 1-4 THE BIGGEST BIOLOGICAL DISTINCTION – THE PROKARYOTES AND THE 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. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  What is the difference between a eukaryote and a prokaryote? 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Prokaryotes and Eukaryotes Prokaryote – Greek derivation meaning “before the nucleus”; unicellular; includes bacteria and cyanobacteria; 1-3 micrometers Eukaryote – Greek derivation meaning “true nucleus”; contains a well-defined nucleus surrounded by a nuclear membrane; unicellular (e.g. yeasts and Paramecium) or multicellular (e.g. animals and plants); 10-100 micrometers 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Prokaryotes and Eukaryotes organelle – is a part of the cell that has a distinct function and is surrounded by its own membrane within a cell. Plasma/Cell membrane is the only membrane found in the prokaryotic cell. cell membrane - consists of a double layer (bilayer) of lipid molecules with a variety of proteins embedded in it. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Prokaryotes and Eukaryotes cytoplasm – refers to the portion of the cell outside the nucleus cytosol – is the aqueous portion of the cell that lies outside the membrane-bounded organelles. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  PROKARYOTIC CELLS How is prokaryotic DNA organized without a nucleus? 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  The genome is attached to the cell membrane. Before a prokaryotic cell divides, the DNA replicates itself, and both DNA circles are bound to the plasma membrane. The cell then divides, and each of the two daughter cells receives one copy of the DNA. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  How is prokaryotic DNA organized without a nucleus? The cytosol (the fluid portion of the cell outside the nuclear region) frequently has a slightly granular appearance because of the presence of ribosomes (ribonucleoprotein particles). cell membrane – plasma membrane; an assemblage of lipid molecules and proteins. cell wall – made up mostly of polysaccharide material; serves as protection for the cell. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  EUKARYOTIC CELLS What are the most important organelles? 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Nucleus – surrounded by nuclear double membrane (nuclear envelope); nucleolus is rich in RNA; site of RNA synthesis Nucleolus – rich in RNA Chromatin – an aggregate of DNA and protein. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Mitochondrion – has a double membrane. The outer membrane has a fairly smooth surface, but the inner membrane exhibits many folds called cristae. The space within the inner membrane is called the matrix. It contains enzymes that catalyze important energy- yielding reactions; 1 μm in diameter and 2 to 8 μm in length 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Endoplasmic Reticulum (ER) – a part of continuous single- membrane system throughout the cell; attached to the cell membrane and to the nuclear membrane Rough ER – is studded with ribosomes Smooth ER – does not have ribosomes bound to it. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Chloroplasts – found only in green plants and green algae; up to 2 micrometers in diameter and 5-10 micrometers in length; contain a characteristic DNA. Grana – photosynthetic apparatus; membranous bodies stacked within the chloroplast. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  EUKARYOTIC CELLS What are some other important components of cells? 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Golgi apparatus – separate from the ER but is frequently found close to the smooth E; a series of membranous sacs; involved in the secretion of proteins from the cell. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Lysosomes– are membrane-enclosed sacs containing hydrolytic enzymes that could cause considerable damage to the cell if they were not physically separated from the lipids , proteins, or nucleic acids that they are able to attack. Peroxisomes – are similar to lysosomes; their principal characteristic is that they contain enzymes involved in the metabolism of hydrogen peroxide (toxic to the cell) Catalase – an enzyme which occurs in peroxisomes, catalyzes the conversion of 𝐻2 𝑂2 to 𝐻2 𝑂 and 𝑂2. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Glyoxysomes – are found in plant cells only; contain the enzymes that catalyze the glyoxylate cycle, a pathway that converts some lipid to carbohydrate with glyoxylic acid as an intermediate. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  Cytoskeleton – or microtrabecular lattice, is connected to all organelles; maintains the infrastructure of the cell. 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes  1-5 How We Classify Eukaryotes and Prokaryotes  FIVE-KINGDOM CLASSIFICATION SYSTEM How do scientists classify living organisms today? 1-4 The Biggest Biological Distinction – The Prokaryotes and the Eukaryotes 1-5 How We Classify Eukaryotes and Prokaryotes  EUKARYOTIC ORIGINS Did symbiosis play a role in the development of eukaryotes? 1-5 How We Classify Eukaryotes and Prokaryotes  EUKARYOTIC ORIGINS Symbiosis plays a large role in current theories of the rise of eukaryotes. Mutualism – benefits both species involved. Parasitic Symbiosis – one species gains at the other’s expense 1-5 How We Classify Eukaryotes and Prokaryotes  EUKARYOTIC ORIGINS Endosymbiosis – in hereditary symbiosis, a larger host cell contains a genetically determined number of smaller organisms. Example: cyanobacteria contained within the host organism 1-5 How We Classify Eukaryotes and Prokaryotes  EUKARYOTIC ORIGINS EUKARYOTIC ORIGINS 1. Bacteria 2. Archaea 3. Eukaryotes 1-5 How We Classify Eukaryotes and Prokaryotes 1-6 Biochemical Energetics  THERMODYNAMIC PRINCIPLES What is the source of energy in life processes? 1-6 Biochemical Energetics  Biochemical Energetics The 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 (reduction). Non-photosynthetic organisms – consume these carbohydrates and use them as energy sources (oxidation). 1-6 Biochemical Energetics  Biochemical Energetics A reaction that takes place as a part of many biochemical processes is the hydrolysis of the compound ATP. 1-6 Biochemical Energetics 1-6 Biochemical Energetics 1-6 Biochemical Energetics  ENERGY CHANGES What kinds of energy changes take place in living cells? 1-6 Biochemical Energetics  Energy Changes Photosynthesis requires light energy from the Sun. Some organisms, such as several species of fish, are striking examples of the use of chemical energy to produce electrical energy. The formation and breakdown of biomolecules involve changes in chemical energy. 1-6 Biochemical Energetics 1-6 Biochemical Energetics  Energy Changes Spontaneous – in thermodynamics, characteristic of a reaction or process that takes place without outside intervention. 1-6 Biochemical Energetics  SPONTANEITY IN BIOCHEMICAL REACTIONS How can we predict what reactions will happen in living cells? 1-6 Biochemical Energetics  Spontaneity in Biochemical Reactions The most useful criterion for predicting the spontaneity of a process is the free energy, which is indicated by the symbol, G (at constant temperature and pressure) 1-6 Biochemical Energetics  Spontaneity in Biochemical Reactions The free energy of a system decreases in a spontaneous (energy-releasing) process, so ∆𝐺 is negative ∆𝐺 < 0. Such process is called exergonic, meaning that energy is released. 1-6 Biochemical Energetics  Spontaneity in Biochemical Reactions When the change in free energy is positive ∆𝐺 > 0 , the process is nonspontaneous. For a nonspontaneous process to occur, energy must be supplied. Nonspontaneous processes are also called endergonic, meaning that energy is absorbed. 1-6 Biochemical Energetics  Spontaneity in Biochemical Reactions For a process at equilibrium, with no net change in either direction, the change in free energy is zero ∆𝐺 > 0. 1-6 Biochemical Energetics  Spontaneity in Biochemical Reactions 1-6 Biochemical Energetics  LIFE AND THERMODYNAMICS Is life thermodynamically possible? 1-6 Biochemical Energetics  Life and Thermodynamics 1st Law of Thermodynamics – it is impossible to convert energy from one form to another at greater than 100% efficiency (law of conservation of energy). 2nd Law of Thermodynamics – even 100% efficiency in energy transfer is impossible 1-6 Biochemical Energetics  Life and Thermodynamics The two laws of thermodynamics can be related to the free energy by means of a well-known equation: ∆𝐺 = ∆𝐻 − 𝑇∆𝑆 G = free energy; H = enthalpy; S = entropy 1-6 Biochemical Energetics  Life and Thermodynamics 1st Law – focus on the change in enthalpy, ∆𝐻, which is the heat of a reaction at constant pressure. 2nd Law – focus on changes in entropy, ∆𝑆. Entropy changes are particularly important in biochemistry. 1-6 Biochemical Energetics  Life and Thermodynamics Cells use a lot of energy to fight the natural tendency toward dispersion into many different arrangements to keep the cell structure intact. 2nd Law – In any spontaneous process, the entropy of the Universe increases (free energy decreases). Entropy changes are important in determining energetics of protein folding. 1-6 Biochemical Energetics  Thanks! Any questions? 117  REFERENCES: Campbell, M.K. & Farrell, S. (2018). Biochemistry (9th ed.). Cengage Learning. Garrett, R.H. & Grisham, C.M. (2024). Biochemistry (7th ed.). Cengage Learning. 118 1-2 Chemical Foundations of Biochemistry