Biochemistry Chapter I-III PDF

**[PRELIM DISCUSSION]** **I: INTRO: THE ROLE OF BIOCHEMISTRY IN THE LIFE SCIENCES** **II: MICROSCOPE** **III: LIVING CELL** **[I: THE ROLE OF BIOCHEM IN THE LIFE SCIENCES]** THE NATURE OF BIOCHEMISTRY Our body is an incredible chemical factory. It is also a living machine that can do many diff...

**[PRELIM DISCUSSION]** **I: INTRO: THE ROLE OF BIOCHEMISTRY IN THE LIFE SCIENCES** **II: MICROSCOPE** **III: LIVING CELL** **[I: THE ROLE OF BIOCHEM IN THE LIFE SCIENCES]** THE NATURE OF BIOCHEMISTRY Our body is an incredible chemical factory. It is also a living machine that can do many different kinds of jobs. To stay in good condition, it needs many specific chemicals compound. Our body is made up of millions of tiny cells and thousands of chemical reactions. The study of these reactions and the chemicals that they produce is called **BIOCHEMISTRY** -- is the chemistry of living things and life processes. Biochemistry is the study of compounds, chemical reaction, and molecular interactions that are involved in the production, maintenance and reproduction of living organisms. Like all scientific endeavors, it operates on the premise that all changes and interactions that occur in the physical universe follow certain fixed rules. ATTRIBUTES OF LIFE Some characteristics of living things that ensure survival: **Adaptation** -- or the presence of body structures that make living things fit to live in its habitat. Adaptation is a way for an entire population of organisms to respond to long term changes in their surroundings. Adaptation is also passed from generation to generation. **Growth and Repair** -- growth is the ability to add new tissue, while repair is the ability to replace damage parts. **Reproduction** -- is the ability to beget offspring, ensuring propagations and continuance of the species. Is the formation of new individuals for the propagation of the species. Without reproduction, the species will die out and become extinct. **Metabolism** -- is sum of all the biological and chemical activities that provide energy. Constructive metabolism is called anabolism, while destructive metabolism is catabolism. **Complexity and Organization** -- complexity refers to elaborate structures needed to carry out laborious functions like metabolism. Organization is putting the different body structures into order, so that the organism can function effectively and efficiently. **Regulation** -- is the ability to keep the functions under control through the use substances like hormones and enzymes. **All living organisms possess a characteristic size and shape** -- ex: an ant can never become as big as an elephant. **Responsiveness to stimuli or Sensitivity** -- is the ability to respond favorably or unfavorably to its environment. **Locomotion** -- is the ability to move on its initiative, under its control. **Variation and Change** -- explains why no two organisms are exactly alike (variation) and no organism remains unchanged forever. Adaptation and evolution are mechanisms of change. **Development** -- includes all changes undergone by an organism through time. It starts with fertilization and ends with death. Development involves growth and differentiation. Differentiation is a process that changes the cell structure to make it functional. For example -- after fertilization, generalized cells specialize to become cells with specific functions -- skin cells, nerve cells, etc... THE CHEMICALS OF LIFE: All living organisms are predominantly constructed from carbon, oxygen and hydrogen, together with some inorganic elements like nitrogen, phosphorous, and sulfur. - Water All life forms, from the simplest bacteria to the most complex multicellular plants and animals contain water. Human cells are composed of about 70% water, over 80% in blood and 60-70% of the body as a whole. - Organic compounds Nucleic acids (DNA and RNA), proteins, carbohydrates, fats and lipids - Inorganic elements Bulk elements (N, Na, Mg, P, S, Cl, K, Ca) requires in relatively large amounts. Trace elements like; Fe, Zn, I. **[II: THE MICROSCOPE]** Is an optical instrument with a combination of lenses used to observed small objects or substances under magnification. Is an instrument for looking a small things or an instrument for magnifying and observing every small objects. The word microscope comes from the ancient Greek words ***MIKROS*** which means "small" and ***SKOPIEN*** which means "to look at" or "to view". This was coined by Giovanni Farber in 1965, exactly 48 years before Anton Van Leeuwenhoek developed a functional microscope in 1673. There is no record or history as to who invented the first microscope. However, in the 13^th^ century a monk named Roger Bacon learned how to grind glass to make spectacles. In 1590, Zacharias Jansen, devised the first compound microscope, composed of a convex objective and a concave eyepiece. In 1611 Johannes Kepler suggested that a compound microscope which uses convex lenses on both objectives and the eyepiece be constructed, but apparently he did not construct one. But in 1628 Christopher Schanir constructed Kepler microscope and used it for usual observation and micro projection. It became the prototype and modern microscope. In 1665 Robert Hooke, is the first to use the compound microscope for scientific purposes. 1n 1673 Anton Van Leeuwenhoek, a Dutch Merchant, he recognized the first microscopist who made the first copes. In 1684 Christians Hugeness, invented the simple but effective 2-lens eyepiece microscope. In 1813 -- 1881 Charles A. Spurer, designed the advance microscope objectives by introducing higher numerical aperture. Eventually, the modern microscopes were invented from the idea of the simple one. Francis A. Wenham, 1853 -- dark field microscope Fritz Zernike, 1935 -- phase contrast microscope E.N. Harvey and A.L. Leomis -- centrifuge microscope Knoll, Ruska, Rodenbergh, 1935 -- electron microscope Haws Mahl, 1939 -- has finally made more powerful microscope. TYPES OF MICROSCOPE: - Simple or single Microscope -- consists of a single lens; the image of an object is projected and enlarged but not inverted. - Compound Microscope -- consists of a system of lenses, the objectives and the eyepiece or ocular. It maybe monocular with one ocular, or binocular with two oculars - Electron Microscope -- a microscope that uses electrons rather than visible light to irradiate clear, magnified images - Stereoscopic Microscope -- a binocular form of microscope with double objectives, designed to give three dimensional view of the specimen. PARTS OF THE MICROSCOPE: ***1. Mechanical parts*** -- consists of those parts of a microscope responsible for its manipulations namely: Base -- the U-shaped or Y-shaped structure on which the microscope firmly rest in place; it support the microscope. Pillar -- the post or vertical extension of the base to which the arm is attached; it supports and holds the stage. Arm -- the curved structure that connects the base and the body tube; serves as the handle of the microscope and at the same time supports the optical mechanisms. Stage -- the platform upon which the object (slide) is placed when being examined. Substage -- found below the stage and usually composed of an Abbe condenser above and an iris diaphragm below. Body Tube -- a hollow cylinder that connects the ocular to the objectives Inclination Joint/Screw -- movable hinge that attaches the frame of the microscope to the base and is used for tilting the microscope Draw Tube -- a small tube attached above the body tube wherein the ocular or the eyepiece is placed. Revolving Nosepiece -- attached to the base of the body tube and holds the two objectives; LPO and HPO; it facilitates shifting of the objectives. Dust Shield -- prevents dust from falling into the stage where the slide is. Stage Clip -- that hold the slide securely in position. Adjustment Knob -- consists of two pairs of knobs which when turned clockwise or counter clockwise: Course Adjustment Knob -- this is the upper larger knob used to bring the object into focus, so it can be clearly seen. Fine Adjustment Knob -- this is the lower smaller knob used for more delicate focusing. ***2. Illuminating parts*** -- consists of any means employed to direct light upon the object under observation, namely: Mirror -- the double-faced mirror below the substage screwed to the pillar. One of the faces is plain and the other is concave. Condenser -- a substage optical instrument which concentrates light from the mirror into the specimen. Diaphragm -- opaque plates with openings of various sizes for regulating the illumination of the objects to be examined. ***3. Magnifying parts*** -- consists of those parts of a microscope responsible for the magnification or enlargement of the objects so that the detailed parts may be studied: Eyepiece or Ocular -- a small tube consisting of lenses to indicate relative powers of magnification Objectives -- three objectives attached to the revolving nosepiece: - LPO -- shorter tube used to focus the objects in general. - HPO -- longer tube to focus the objects in detail. - OIO -- longer tube to focus specific parts of the objects in detail. A drop of oil is placed on the slide for better refraction. THE USE OF MICROSCOPE In focusing, adjust the relation of the lenses to the object so that a clear image and the object may be seen thru the ocular. The image of the object cannot be seen unless the object is at the proper distance from it or is in focus. ***Rules to be observed in focusing:*** - Adjust the mirror. Be sure that the whole field you see is uniformly lighted, and see to it that the diaphragm is opened. - Focus upward for there is danger of injuring the lens and specimen if you focus downward. - See that the objective (HPO, LPO, and OIO) is in line with the body tube. - When the HPO is in the position, never focus with the course adjustment, use only the fine adjustment knob. - In working with artificial light, as from an electric light, use always the concave mirror. - Clip the slide in place in order that the slide will not move at the slightest movement made on the table. - Above all, keep both eyes open. To close one eye while focusing will strain your eyes. CARE OF THE MICROSCOPE: - Never touch glass parts of the microscope with your fingers as they leave marks and blur the image. - Clean lenses with soft tissue, never with hard paper or any other similar material as it will damage the lenses. - Do not allow liquids to come in contact with any parts of the microscope. - Always use a cover glass when examining object. - Do not remove the pointer. - Carry the microscope with both hands. See to it that the base is being supported by one hand and the other on the handle. Do not swing the microscope. - Always seek the help of the professor when you are in doubt regarding the use of the parts of the microscope **[III: THE LIVING CELLS]** It is more important to begin our discussion in biochemistry with the study of cell structure and functions because cells not test tube or beakers are the natural settings of most biochemical reactions. A major difference between biochemistry and ordinary chemistry is that biochemical reactions take place within the constraints imposed by the size of cells and their internal compartments, as well as the physical and chemical condition that are compatible with cellular life. The structural unit of all living things is the **CELL.** Cells are the smallest unit of living things. Inside the cells are highly specialized structures called organelles. The nucleus is a centrally located organelle that contains the cell's genetic material. The material surrounding the nucleus is the cytoplasm, or the cytosol, which is enclosed by the cell membrane. Every cell is enclosed in a membrane and plant cells also have walls made of cellulose. Based on both microscopic and biochemical differences, living cells are divided into **2 major classes:** **Prokaryotic Cells (bacteria, viruses...) -** simplest and smallest cells - 1^st^ to arise in biological evolution - There are some 20 different families of prokaryotic cells, consists of about 3000 species of bacteria, some of which are pathogenic but many are also beneficial. - They lack a class of protein termed HISTONES - They multiple by asexual divisions **Eukaryotic Cells (animals and plants) -** they are much larger, more complex and show a wider range of diversity and differentiation. - This cell arose a billion years after the prokaryotes. - A type of cells found in an multicellular animals, plants and fungi. - Have a well-defined nuclear membrane and a variety of intracellular structures and organelles. - Undergo asexual division, but this occurs by a much more complex process called **MITOSIS** -- is a cell replication resulting in the formation of daughter cells identical to the parent cells. **Two Phases of Mitosis:** - Nuclear division (karyokinesis) - Cytoplasmic division (Cytokinesis) When the cell is not dividing, it is at **INTERPHASE** -- the resting stage of mitosis. **Different Stages of Plant and Animal Mitosis:** - **Prophase** - **[Metaphase]** (middle) - **[Anaphase]** (apart) - **[Telophase]** (final) THE CELL CYCLE In eukaryotes, the cell cycle includes a series of regulated events. The first stage is the M phase, where the process of mitosis occurs. Mitosis is the condensation, alignment, and separation of chromosomes followed by the division of a parent cell into two daughter cells. DNA replication occurs in the S (synthesis) phase and the M phase. G~1~, S, and G~2~ are referred to as the interphase, or the resting stage which occupies the greater part of the total time of a cell cycle. An unusual proliferation of cells in the M stage is an indicator of cancer. When the cell is not dividing, it is at INTERPHASE -- the resting stage of mitosis. Interphase: - The stage between successive mitosis - The cell is in its normal state wherein the nucleus is observed as still-bounded by the nuclear membrane which encloses a nucleolus and the granular chromatin aside from the nucleoplasm - The period of exposure of genetic material, proliferation of RNA and protein synthesis in the cytoplasm. Prophase (1st stage of mitosis): - Both cytokinesis and karyokinesis happens simultaneously - Centriole divides into two - one of which migrates along the nuclear membrane until they lie opposite to each other. - As the moving Centriole travel towards the opposite pole, it formed a spindle fibers in the cytoplasm - Toward the end of this stage, the nuclear membrane and the nucleolus totally disappear. Metaphase (2nd stage): - The chromosomes reach their most compact shape. Chromosomes are moved to the spindle equator. The end of metaphase is marked by the alignment of all the chromosomes at the equatorial plane Anaphase (3rd stage): - Two events are characterized: separation of sister chromatids of each chromosomes; and their movement to opposite poles Telophase (last stage): - Condensation is reversed, so that the chromosomes now becomes extended in the thread-like form - The nuclear membrane is reconstituted and the nucleolus disappears. SIMILARITIES OF PLANT AND ANIMAL CELLS: - They are both eukaryotic, that means they have a proper nuclei. - It also contains cytoplasm. Perhaps the most important things to be found in cytoplasm are mitochondria. Mitochondria also contain a bit of DNA which control how they work. - They have also a cell membrane around them. DIFFERENCES: - Plant cells are surrounded by a cell wall made of cellulose. - Animal cells are different; they do not have cell wall that means that all animals have to excrete excess water. - Plant cells contain chloroplast. These contain a green chemical called **CHLOROPHYLL** -- is necessary for photosynthesis. - Most of the space inside the plant cells contains large vacuoles, while animal cells never contain large vacuoles. - Plant cells usually have a regular shape whereas; animal cells usually have irregular shape. Only plant cells have: Cell wall, Chloroplast, Large vacuoles and Regular shape ANIMAL CELLS **Three Main Regions:** - Nucleus -- usually located near the center of the cells. It is surrounded by the semi fluid cytoplasm. - Cytoplasm -- is the cellular materials outside the nucleus and inside the plasma membrane. Is the site of most cellular activities, so it is called the factory area of the cells. Three major elements: cytosol, organelles, inclusions. - Plasma membrane (cell membrane or cytoplasmic membrane) -- the structure of the plasma membrane consists of 2 lipids layers arranged "tail to tail' in which CHON molecules float. MAJOR LIPIDS IN MAMMALIAN MEMBRANES: - Phospholipids -- present in all cells, plant as well as animals and the 2^nd^ most abundant naturally occurring lipids. Most of the phospholipids are composed of fatty acid, nitrogenous base, phosphoric acid and either glycerol (phosphoglycerides) or sphingosine (sphingomyelin). - Free Cholesterol -- the most common sterol in membranes, it is generally more abundant toward the outside of the plasma membrane. - Glycosphingolipids -- sugar containing lipids such as Cerebrosides and Gangliosides. All three lipids are amphipathic -- that is they have a hydrophilic end and hydrophobic end. PROCESSES BY WHICH SUBSTANCES ARE TRANSFERRED ACROSS CELL MEMBRANES: **Diffusion** -- the movement of any substance from an area where it is more concentrated to an area where it is less concentrated. **Osmosis** -- a type of diffusion, but involving only the movement of water across a membrane and therefore proceeds from the more dilute to the more concentrated solution. **Facilitated diffusion --** moves substances in and out of cells from higher to lower concentration of a particular solutes **Active transport** -- moves substances across the cell membrane against the concentration gradient, - from lower to higher concentration. This results in the accumulation of substances on one side of the cell membrane. ATP is required. The movement of AA from the SI to the blood is an example of active transport. The Na-K pump is another example. **Phagocytosis** -- is the term used when solid particles are ingested. It is the process by which a cell engulfs a foreign substance or body. **Pinocytosis** -- the pumping of water across the membrane. It is similar to phagocytosis, except the smaller vesicles containing liquids are formed. **Question:** Why is meant by selectively permeable, and why is this term applied to the cell membrane? **Answer:** Permeable means that substances can pass through. Selectively permeable means that certain substances can pass through but not others... One of the important functions of the cell membrane is to regulate which substances are admitted into and out of the cell. FUNCTIONS OF THE CELLS: The cell is the basic unit of life, and as such carries out all processes pertinent to the maintenance of life. These functions are: **For protection and support** -- it manufactures and secretes various molecules that protect and support the body of the organism, e.g.., bone cells that protect vital organs and supports body mass **For movement**, e.g., muscle cells **For communication** -- it produces and receives chemical and electrical signals that enable them to communicate with each other, e.g., nerve cells **For cell metabolism and energy release** -- which include all chemical reactions that occur within cells resulting in the production of energy used for cell activities, e.g. , muscle contraction, heat production **For storage of genetic information** -- so it can be accurately transmitted to the succeeding generation. SEVEN MAJOR CELLULAR COMPARTMENTS COMMON TO MOST EUKARYOTIC CELLS: **Cytosol** Consists of all the space outside the cellular organelles and generally represents 50-60% of the total cell volume in eukaryotes. Also contains metabolic pathways for the synthesis of storage forms of fuel: - TAG (triglycerides) -- storage forms of fatty acids - Glycogen -- major storage forms of CHO (carbohydrates) **Nucleus** It contains nearly all the DNA of eukaryotic cells, and generally ovoid or spherical in shape. It is also bounded by the inner and outer nuclear membrane containing nucleus pores. It is surrounded by a nuclear envelope. Inside the nucleus is the nucleolus -- which stains more densely, because of its rich content of RNA. Nucleolus is an RNA factory. Rest of the nucleus contains chromatin. It is called as the *INFORMATION CENTER OF THE CELL.* *Main Parts of the Nucleus:* - Nuclear Membrane / Nuclear Envelope -- serves as the outermost part of the nucleus. - Karyolymph / Nuclear Sap / Nucleoplasm -- fluid portion of the nucleus. - Chromatin -- darkly staining materials suspended within the nuclear sap. - Nucleolus -- rounded bodies rich in rRNA. **Endoplasmic Reticulum** In the cytoplasm of nearly all eukaryotic cells, there is a very complex 3D maze of membrane channel -- ER. It forms many fold and convolutions throughout the cytoplasmic space. The space enclosed within the ER called CISTERNAE -- serves as channel for the transport of various products through the cells. *Two Functionally Distinct Regions of ER:* - Rough ER -- This is studded with ribosomes on the cytoplasmic side of the membrane. - Smooth ER -- This is physically a portion of the same membrane but lacks any attached ribosomes. Whereas Rough ER is organized in stacks of flattened sacs called CISTERNAE, smooth ER consists of a meshwork of fine tubules. **Golgi apparatus** Also called as dictiosomes and golgiosomes. It consists of stacks of flattened, disc shaped cisternae with associated small vesicles. It usually located near the cell nucleus. The accurate sorting or "packaging" of CHONS for selective export is one of their major functions. Called as the secretory organelles. **Mitochondria** It is the 2^nd^ largest organelle of the cells. It may appear as spheres, rods, cigar shaped. POWER HOUSE OF THE CELL ***--*** because of ATP that provides energy for all cellular works. **Lysosomes** The small round or ovoid bodies that contains hydrolytic enzymes (capable for digesting). SUICIDE BAG -- literally it is "Breakdown Bodies" it is capable of digesting worn out or non-usable cell structures and most foreign substances that enter the cells. **Peroxisomes** This single membrane surrounded organelle is somewhat larger than lysosomes. Also called as microbodies. **BLOOD** - Is the river of life that surges within us. It transports everything that must be carried from one place to another within the body -- nutrients, wastes and body heat. - A sticky opaque fluid with a characteristic metallic taste. - Depending on the amount of oxygen it is carrying, the color of blood varies from scarlet (0~2~ rich) to dull red (0~2~ poor). - Is heavier than water and about 5x thicker, or more viscous. - It is slightly alkaline with a pH between 7.35-7.45. - Temperature (38'C or 100'F) is always slightly higher than body temp. A complex connective tissue in which living blood cells -- ***FORMED ELEMENTS (45%)*** are suspended in a nonliving fluid matrix called ***PLASMA (55%)*** - approximately 90% water, is the liquid part of the blood. THE COMPOSITION OF BLOOD: ***A. PLASMA*** [Constituents'] [major functions] - Water solvent for carrying other substances - Salts (Electrolytes - Na, K, Ca, Mg, Cl, Bicarbonates) Osmotic balance, pH buffering, and regulation of membrane permeability - Plasma proteins: - Albumin osmotic balance, pH buffering - Fibrinogen - Substances transported by blood: - Nutrients (glucose, FA, vitamins, AA) - Waste products of metabolism (urea, uric acid) - Respiratory gases (O~2~ and CO~2~) - Hormones ***B. FORMED ELEMENTS*** [cell type] [\#(per mm^3^ of blood)] [functions] RBC 4-6 M transport O~2~ and CO~2~ WBC 4000-11,000 defense and immunity Platelets 250,000-500,000 blood clotting **ERYTHROCYTES** A ↓ in the O~2~ carrying ability of the blood, whatever the reason is ***ANEMIA*** -- it may be the result of lower than normal \# of RBC or abnormal or deficient hemoglobin content in the RBC. An excessive or abnormal ↑ in the \# of RBC is ***POLYCYTHEMIA*** - may result from BM cancer (polycythemia vera). It may also be a normal physiological response to living at high altitudes where air is thinner and less O~2~ is available. **LEUKOCYTES** A total WBC count above 11,000 cells/mm^3^ is referred to as ***LEUKOCYTOSIS*** -- indicates that a bacterial or viral infection is stewing in the body. The opposite condition is ***LEUKOPENIA*** -- an abnormally low WBC count. It is commonly caused by certain drugs such as corticosteroids and anticancer agents. TERMS: - Hematopoiesis - a blood cell formation occurs in red BM, or myeloid tissue. - Hemocytoblast - Stem cells that give rise to all the formed elements of the blood. - Hemostasis - Stoppage of blood flow. - Hemoglobin - O2 transporting pigment of erythrocytes - Hemophilia - an inherited clotting defect caused by absence of a blood clotting factor. - Erythropoiesis - the process of erythrocyte formation. - Erythropoietin - rate of erythrocytes production controlled by a hormone. - Thrombus - a fixed clot that develops and persists in an unbroken blood vessel. - Thrombocytopenia - results from an insufficient \# of circulating platelets.