Biomolecules (N) PDF

ENERGY FLOW IN THE CELL MOLECULAR COMPOSITION OF CELLS LEARNING COMPETENCIES THE LEARNERS: - CATEGORIZE THE BIOLOGICAL - EXPLAIN THE ROLE OF EACH - DETECT THE PRESENCE OF MOLECULES ACCORDING TO BIOLOGICAL MOLECULE IN BIOLOGICAL MOLECULES IN FOOD...

ENERGY FLOW IN THE CELL MOLECULAR COMPOSITION OF CELLS LEARNING COMPETENCIES THE LEARNERS: - CATEGORIZE THE BIOLOGICAL - EXPLAIN THE ROLE OF EACH - DETECT THE PRESENCE OF MOLECULES ACCORDING TO BIOLOGICAL MOLECULE IN BIOLOGICAL MOLECULES IN FOOD THEIR STRUCTURE AND FUNCTION SPECIFIC METABOLIC PROCESSES PRODUCTS ABUNDANT ELEMENTS IN THE HUMAN BODY (Source: http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/chemistry/elementsorgnsm.jpg)  CHEMICAL COMPOSITION OF LIVING BEINGS BIOGENIC ELEMENTS – the building blocks of all living organisms; the most abundant being oxygen, carbon, hydrogen, and nitrogen (96% of total body mass) CARBON – has the unique potential to generate a variety of chemical combinations that are essential for the makeup of the molecules of living organisms  CATEGORIES OF BIOGENIC ELEMENTS PRIMARY ELEMENTS – include O, C, H, N, & the less abundant, Ca & P (98% of total body mass) SECONDARY ELEMENTS – comprise K, Su, Na, Cl, Mg, & Fe; have much lower relative quantities; exist as salts, inorganic ions, & part of organic molecules TRACE ELEMENTS – microconstituents/oligoelements; present in very small quantities; include I, Cu, Mn, Co, Zn, Mo, Se  BIOGENIC ELEMENTS PRIMARY ELEMENTS ELEMENT RELATIVE ELEMENT RELATIVE ABUNDANCE ABUNDANCE Oxygen 65.0 Nitrogen 3.0 Carbon 18.5 Calcium 1.5 Hydrogen 10.0 Phosphorus 1.0  BIOGENIC ELEMENTS SECONDARY ELEMENTS ELEMENT RELATIVE ELEMENT RELATIVE ABUNDANCE ABUNDANCE Potassium 0.30 Chlorine 0.15 Sulfur 0.25 Magnesium 0.05 Sodium 0.20 Iron 0.005  BIOGENIC ELEMENTS OLIGOELEMENTS ELEMENT RELATIVE ELEMENT RELATIVE ABUNDANCE ABUNDANCE Fluorine 0.001 Zinc Traces Cuprum 0.0002 Cobalt Traces Iodine 0.00004 Molybdenum Traces Manganese 0.00003 Selenium Traces  BIOLOGICAL COMPOUNDS Among the inorganic compounds, WATER is of exceptional importance due to its numerous biological roles. MUSCLE BONE BRAIN LIVER WATER 75.0 22.0 77.0 70.0 CARBOHYDRATES 1.0 Scarce 0.1 5.0 LIPIDS 3.0 Scarce 12.0 9.0 PROTEINS 18.0 30.0 8.0 15.0 OTHER ORGANIC 1.0 Scarce 1.5 1.0 SUBSTANCES OTHER 1.0 45.0 1.0 Scarce INORGANIC SUBSTANCES Data from the table shows that there are only three elements that are abundant in the body... More than 90% of the human body weight is provided by 1. OXYGEN 2. CARBON 3. HYDROGEN Where do we get these 3 elements? WATER WE DRINK FOOD WE EAT AIR WE BREATHE HETEROTROPHS Heterotrophs, such as human beings, obtain energy and raw materials from FOOD. These are IMPORTANT for cell growth, cell division, metabolism, repair, and maintenance of the body.  Nutrients can be classified as either ORGANIC NUTRIENTS (i.e., those that contain carbon such as carbohydrates, fats, proteins, vitamins, and nucleic acids) or INORGANIC NUTRIENTS (i.e., those that do not contain carbon such as water and mineral salts). CHEMISTRY OF THE CELL  STRUCTURED AROUND 5 PRINCIPLES: 1. The importance of CARBON. 2. The importance of WATER. 3. The importance of SELECTIVELY PERMEABLE MEMBRANES. 4. The importance of SYNTHESIS by polymerization of small molecules. 5. The importance of SELF-ASSEMBLY.  CHEMISTRY OF CELLS CELLS – composed of water, inorganic ions and carbon-containing (organic) molecules 16 MOLECULAR COMPOSITION OF CELLS: a.WATER – abundant molecule (≥ 70% of cell mass) -it is polar and it can form H-bonds with each other or with polar molecules  WATER POLARITY cohesiveness, temperature-stabilizing capacity and solvent properties of water. PROPERTIES OF WATER It stabilizes body temperature. The high capacity of water allows it to absorb and release large amounts of heat before changing temperature. The high heat vaporization allows great cooling effect. Its high heat fusion prevent organisms from freezing at a low temperature.  It serves as protection for organisms. It acts as lubricant or cushion for organisms. It is necessary in chemical reactions within the organism. Most of the chemical reactions necessary for life do not take place unless the reacting molecules are dissolved in water. Water also directly participates in many chemical reactions.  It serves as transport molecules in the body of an organism. Polar solvent properties: dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport medium.  b. INORGANIC IONS – Na⁺, K⁺, Mg2⁺, Ca2⁺ , phosphate (HPO42¯), Cl¯ and bicarbonate (HCO3¯) - 1% or less of the cell mass -these ions are involved in number of aspects of cell metabolism c. ORGANIC MOLECULES - 80-90% of the dry weight of most cells -carbohydrates, lipids, proteins, and nucleic acids  ORGANIC MOLECULES Always contain Carbon (C) and Hydrogen (H) Capable of forming 4 covalent bonds Carbon can bind with hydrogen, nitrogen, oxygen, and itself! Forms long chains, branched, rings, etc Proteins, Carbohydrates, Lipids etc are macromolecules Many molecules joined together Monomer Simple molecules Polymer Large molecules formed by combining monomers  POLYMER FORMATION Making big molecules from small molecules Dehydration Synthesis Water is produced as monomers are combined together  POLYMER BREAKDOWN Breaking big molecules into small molecules Hydrolysis Water breaks up the bonds in another molecule Requires enzymes (helping molecules) THE IMPORTANCE OF SYNTHESIS BY POLYMERIZATION Macromolecules are responsible for most of the form and function in living systems BIOMOLECULES (organic molecules or macromolecules) due to their large size and complex nature, serve as a fuel for the metabolism of organism. BIOLOGICAL POLYMER A. Carbohydrates B. Lipids C. Proteins D. Nucleic Acids FUNCTIONS OF BIOMOLECULES INFORMATIONAL STORAGE STRUCTURAL  BIOLOGICAL POLYMER Proteins Nucleic Polysaccharides Acids Repeating Amino Acids Nucleotides Monosac- Monosac- monomers charides charides Function Informational Informational Storage Structural Examples Enzymes, DNA, RNA Starch, Cellulose Hormones, Glycogen Antibodies A. CARBOHYDRATES the most abundant class of organic - compounds found in living organisms. - CHO (carbon, hydrogen, and oxygen) 1:2:1 ratio - Carbohydrate means “hydrated carbon” - Cn(H2O)n -include simple sugars and polysaccharides They fill numerous roles in living things, such as : a. STORAGE AND TRANSPORT OF ENERGY (eg: starch, glycogen) b. STRUCTURAL COMPONENTS (eg: cellulose in plants and chitin)  Carbohydrates are good sources of raw materials for other organic molecules and energy. One gram of carbohydrates provides 4 food calories or 16 kJ of energy.  How do carbohydrates form? http://www.cengage.com/biology/discipline_content /animations/reaction_types.html HOW ARE CARBOHYDRATES CLASSIFIED? 1. MONOSACCHARIDES (monos means single and sacchar means sugar) 2. DISACCHARIDES (di means two) 3. POLYSACCHARIDES (poly means many) Groups of Carbohydrates Carbohydrates sugars Monosaccharides Disaccharides Polysaccharides (monomers) ( Dimers) (polymers) A. 1. MONOSACCHARIDES - most basic form of carbohydrates - the simplest form of sugar - Formula: C6H12O6 FUNCTIONS: - major cellular nutrient - often incorporated into more complex carbohydrates Names of monosaccharides from 3-7 carbon atoms 3 C - triose 4 C - tetrose 5 C - pentose 6 C - hexose 7 C - heptulose MONOSACCHARIDES - can be classified as ALDOSES or KETOSES according to the placement of chemicals in the structure. ALDOSES KETOSES presence of an aldehyde presence of carbonyl (C=O) group, (CHO) usually at the terminal, or a ketone, usually at second or the first carbon atom carbon atom of the molecule Glucose is an aldose, with an Fructose is a ketose, with a aldehyde located at its ketone functional group at the terminal carbon atom second carbon atom.  A.1.1. GLUCOSE most common carbohydrate “blood sugar” C6H12O6 6C aldose that is the product of photosynthesis and the substrate for respiration that provides energy for cellular activities A.1.2. GALACTOSE a monosaccharide, an important component for sucrose and of blood type. A.1.3. FRUCTOSE is more commonly found together with glucose and sucrose in honey and fruit juices. common name for fructose is levulose or “fruit sugar” sugarcane, sugar beets and corn A.1.4. RIBOSE The ring form of ribose is a component of ribonucleic acid (RNA). A.1.5. DEOXYRIBOSE Deoxyribose is a component of deoxyribonucleic acid (DNA). Derivatives of Monosaccharides ASCORBIC ACID (vitamin C) comes from glucose Sugar alcohols (sorbitol and mannitol), are sweetening agents MONOSACCHARIDES provides immediate energy to the organism that takes them. They are simple sugars (smaller than other types of carbohydrates) Sugary foods and fructose-rich fruits are the best sources of energy for people who drained or tired. A. 2. DISACCHARIDES combination of 2 simple sugars by glocosidic linkage through a process called condensation reaction. Functions: ENERGY SOURCE SWEETENER AND DIETARY COMPONENT  The result of the condensation reaction is the formation of the GLYCOSIDIC BOND (a type of covalent bond that links a carbohydrate molecule to another molecule) A.2.1 SUCROSE combination of Glucose and Fructose C12H22O11 - found in table sugar processed from sugar cane, sweet fruits, and storage roots like carrot A.2.2 MALTOSE - combination of Glucose and Glucose - “malt sugar” - found in sprouting grains, malt-based energy drinks, or beer A.2.3 LACTOSE Combination of Galactose and Glucose “milk sugar” source of energy for infants an enzyme called lactase is required to digest lactose What is lactose intolerance? A. 3. POLYSACCHARIDES forms when hundreds to thousands of monosaccharides are joined by glycosidic linkages are insoluble in water Functions: STORAGE MATERIAL FOR IMPORTANT MONOSACCHARIDES STRUCTURAL MATERIAL FOR THE CELL OR THE ENTIRE ORGANISM LINEAR & BRANCHED POLYSACCHARIDES HEALTH BENEFITS Serve as immediate energy reserves in the body Help stabilize blood sugar and provide vitamins and minerals. (mushrooms, berries, cereals, and grains) PECTIN an important type of polysaccharides. It goes through the digestive system more slowly, making the person fell full for longer. A.3.1. STARCH major form of stored carbohydrate in plants found in plant parts such as potato tubers, corn and rice is composed of a mixture of two substances: -AMYLOSE -AMYLOPECTIN  AMYLOSE an essentially very long, linear polysaccharide molecules consist typically of 200 to 20,000 glucose units  AMYLOPECTIN differs from amylose in being highly branched short side chain of glucose units A.3.2. GLYCOGEN a polymer of glucose units identical to amylopectin; but shorter organized globularly like branches of tree found in animals and fungi found in liver cells and muscle cells A.3.3. CELLULOSE a polymer of glucose units compared to starch, cellulose is unbranched insoluble in water Cellulose - tough sheet-like structures that make up plant and algal cell walls that may be processed to form paper and paper-based products - found in commercially used plants such as abaca, cotton, flax, and pineapple (fabric and paper) - aids man's regular bowel movement - its sugar component is used as a food source A.3.4. CHITIN - used for structural support in the walls of fungi and in (exoskeleton) external skeletons of arthropods (crabs, shrimps, scorpion, and many insects,) - has stronger H-bonds between bordering polymers - has antibacterial and antiviral properties A.3.5. PEPTIDOGLYCAN - used for structural support in bacterial cell walls A.3.6. GLYCOSAMINOGLYCANS are long, unbranched polysaccharide containing repeating disaccharide units are found in the lubricating fluid of the joints and as components of cartilage, synovial fluid, vitreous humor, bone, and heart valves B. LIPIDS Biomolecules containing chains of hydrocarbons (organic compounds that are made up of carbon and hydrogen, and are insoluble in water) Function as long-term energy storage and insulation. B. LIPIDS Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates. Dissolve in nonpolar solvents, such as alcohol or acetone, but not in polar solvents, such as water.  Lipids are loosely defined as groups of organic molecules that are insoluble in water. Their chemical formula vary considerably. Include: fats oils Waxes Phospholipids steroids: sex hormones and cholesterol some vitamins glycolipids (lipids with carbohydrates attached) LIPID STRUCTURE Most lipids are composed of a of glycerol molecule with attached fatty acids GLYCEROL FATTY ACIDS Fatty acid Fatty acid Triglyceride Fatty acid Phospholipid GLYCEROL HYDROPHOBIC END Fatty acid Fatty acid PO FATTY ACIDS 4 HYDROPHYLIC END  Some lipids have a four ringed structure Eg. Cholesterol and other lipids that are derived from cholesterol Types of Lipids TRIGLYCERIDES PHOPHOLIPIDS STEROIDS WAXES STEROIDS Have four fused carbon ring (molecular ring) Help in regulating metabolism, immune response, reproduction, and other essential biological processes. CHOLESTEROL is a sterol (steroid alcohol) one of the most common steroid forms. It usually formed in major organs (brain & blood vessels) Atherosclerosis – hardened the blood vessels thus hamper or block the flow of blood. STEROID HORMONES Progesterone: responsible for changes associated with the menstrual cycle and with differentiation factor for mammary glands Aldosterone: raises blood pressure and fluid volume, increases Na+ uptake Testosterone: male sex hormone synthesized in the testes, responsible for secondary male sex characteristics Estradiol: an estrogen, principal female sex hormone, produced in the ovary, responsible for secondary female sex characteristics Cortisol: involved in stress adaptation, elevates blood pressure and Na+ uptake, numerous effects on the immune system TRIGLYCERIDES Generally knows as FATS Contains a glycerol attached to three fatty acids A fatty acid is composed of a long chain of carbon atoms connected to a carboxylic acid (-COOH). 2 types depending on their nature and origin (Saturated fats and Unsaturated fats)  Saturated fatty acid SATURATED FATS Their fatty acids: have no double bonds between carbon atoms(have maximum number of hydrogen atoms) Straight structure Unhealthy fats usually from animal sources (pork & beef) Also found in butter, cheese and some processed foods. Solid at room temperature(20°C) 81  Unsaturated fatty acid UNSATURATED FATS mostly known as oils Their Fatty acids have: Have some carbon atoms that are double bonded(not fully hydrogenated) Kinked in shape Healthy From plant sources Liquid at room temperature (20°C) Olive oil, coconut oil and corn oil Note: Generally, most animals use fat for long-term energy storage. Your body breaks down fats when you need extra fuel. Excess sugars in your body can also be converted to fats. If you are not physically active, these fats remain unused for a long period for a long time, hence increasing your body weight. PHOSPHOLIPIDS Lipids with a phosphate group Attached on one side of the glycerol backbone are the hydrophobic or nonpolar “tails,” which are composed of two chains of fatty acids. Attached on the other side of the glycerol backbone is the hydrophilic or polar “head,” which is composed of a phosphate group. WAXES Waxes are esters (carboxylic acid derivatives), which are combined from certain alcohols and fatty acids. Waxes are extremely hydrophobic (do not react with water) Waxes are found everywhere in nature Thin coatings on leaves and stems (wax prevents the plant from losing excess water) Furs and feathers of animals (to repel water) Cerumen (earwax, prevents the entry of some materials into the ear canal)  Lipids have the following roles in the body of an organism Serve as the highest energy source. Act as insulators to protect animals from extreme cold. Serves as building blocks of many steroids. Importance: Biological Role Used to store energy (approx 36 KJ/gram) Mitochondrion (false color TEM) Fat cell Lipids are often stored in special adipose tissue, within large fat cells Lipids are concentrated sources of energy and can be broken down (through fatty acid oxidation in the mitochondria) to provide fuel for aerobic respiration  Importance: Biological Role An important structural component of membranes Phospholipids are the primary structural component of all cellular membranes, such as the plasma membrane (false color TEM above).  Importance: Biological Role acts as a shock absorber and good insulator The white fat tissue (arrows) is visible in this ox kidney Fat absorbs shocks. Organs that are prone to bumps and shocks (e.g. kidneys) Stored lipids provide insulation are cushioned with a relatively thick layer in extreme environments. of fat. Increased body fat levels in winter reduce heat losses to the environment.  Importance: Biological Role Water proofing of some surfaces Transmission of chemical messages via hormones Waxes and oils, when secreted on to surfaces provide waterproofing in plants and animals.  Examples of lipids found in the body Fats – found in subcutaneous tissue and around organs Phospholipids – chief component of cell membranes Steroids – cholesterol, bile salts, Vitamin D, sex hormones and adrenal cortical hormones.  Examples of lipids found in the body Eicosanoids – prostaglandins, leukotrienes and thromboxanes Fat-soluble vitamins – Vitamins A, D, E and K Lipoproteins – transport fatty acids and cholesterol in the bloodstream C. PROTEIN Macromolecules that contain C, H, O, N and some S. Central compound necessary for life – building blocks Composed of 20 basic types of amino acids bound together with PEPTIDE BONDS. It maybe dipeptide, containing two amino acids; tripeptide containing three amino acids; polypeptide containing many amino acids.  MADE BY RIBOSOMES DNA Amino acids are JOIN Transcription together by PEPTIDE BONDS RNA Following a sequence Translation dictated by the DNA Polypeptide/Protein  Proteins are polypeptides of hundreds of amino acids AMINO ACIDS are the building blocks of protein molecules It has the following parts Amino group (-NH2) A carboxyl group (COOH) A hydrogen atom A side chain designated by the symbol R attached to the same carbon atom as the hydrogen  Folding of polypeptides to form Proteins Shape of a proteins are important because This determines how they interact with other molecules This determines their particular function  Proteins have different structural levels Primary: determined by the number, kind and arrangement of amino acids Secondary: results from folding or bending of the polypeptide chain caused by the hydrogen bonds between amino acids (helices and pleated sheets) Tertiary: results from the folding of the helices or pleated sheets and the hydrogen bonds formed with water. Quaternary: spatial relationships between two or more proteins that associate to form a functional unit. Primary Structure The simplest of all the proteins Composed only of a linear sequence of Peptide(phosphodiester) bonds amino acids in a peptide chain phe glu tyr ser iso met phe glu Secondary Structure Three dimensional shape created by several hydrogen bonds. Coiling structure as alpha helix and beta pleated sheet (wavelike in appearance) Tertiary Structure Three-dimensional shape of peptide (fibrous or globular in structure) Interactions of the side chains of the different amino acids in the peptide. Quaternary Structure Happens when proteins have more than one polypeptide. Polypeptide chains will create hydrogen bonds with one another in unique patterns to achieve the desired protein configuration. Biological molecules Summary Three Groups of Amino Acids ESSENTIAL AMINO ACIDS – those that cannot be produced by our bodies. NONESSENTIAL AMINO ACIDS – those that can be produced by our bodies. CONDITIONAL AMINO ACIDS – are not vital but may become urgent during health crisis or stress. Most of the essential amino acids are found in beans, legumes, and corn.  CONDITIONALLY ESSENTIAL NONESSENTIAL NONESSENTIALS HISTIDINE ARGININE ALANINE ISOLEUCINE ASPARAGINE ASPARTATE LEUCINE GLUTAMINE CYSTEINE METHIONINE GLYCINE GLUTAMATE PHENYLALANINE PROLINE THREONINE SERINE TRYPTOPHAN TYROSINE VALINE LYSINE  Proteins perform the following roles Regulate chemical reactions (enzymes) Structural proteins provide the framework for many of the body’s tissues Responsible for muscle contraction Serve as food reserves and as transport molecules Form antibodies which protect the body against diseases. Form genes that make organisms different from one another. CATALYSTS eg. lipase REGULATION(hormones) Eg Insulin STRUCTURAL eg.Keratin TRANSPORT: eg hemoglobin TRANSPORT: protein channels or carrier proteins D. NUCLEIC ACID Composed of C, O, H, N and P Largest molecules (being composed of several nucleotide subunits) The basic unit of nucleic acids is the NUCLEOTIDE, which is a monosaccharide with an attached phosphate and organic base.  Five nitrogenous bases contribute to nucleotide structure Adenine (A) Guanine (G) Cytosine (C) Thymine (T) Uracil (U) There are two major classes of nucleic acids – Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) Deoxyribonucleic Acid (DNA) Double stranded helical molecule found in the nucleus of the cell A long molecule that contains coded instruction for cellular activities (growth, reproduction, death, and production) Contains the genetic material of the cell Replicates itself before the cell divides, ensuring genetic continuity Provides instructions for protein synthesis Deoxyribonucleic Acid (DNA) Contains the monosaccharide deoxyribose and the organic bases Adenine Thymine Guanine Cytosine DNA Nucleotides Nucleotide Structure 5’ Phosphate group Nitrogen base (A,G,C,T) Deoxyribose (sugar) 3’ Ribonucleic Acid (RNA) Single-stranded molecule found in both the nucleus and the cytoplasm of a cell. Composed of the monosaccharide ribose and uses the organic base uracil instead of thymine Active in the acquisition of traits. May range from encoding to decoding and regulating the expression of genes, depending on the type of RNA present.  Three kinds of RNA – messenger RNA, transfer RNA and ribosomal RNA Messenger RNA (mRNA) – synthesized from DNA in the genetic material that attaches ribosomes in the cytoplasm and specifies the primary structure of protein. Transfer RNA (tRNA) – an interpreter between nucleic acid and the protein language by picking up specific amino acids and recognizing the appropriate codons in mRNA. Ribosomal RNA (rRNA) – it forms the structure of ribosomes together with nucleic that coordinate the sequential coupling of tRNA molecules to the series of mRNA codons.  DIFFERENCES BETWEEN DNA AND RNA Bases of Comparison DNA RNA Location Nucleus Nucleus and cytoplasm Sugar Deoxyribose Ribose Organic Bases Adenine, Thymine, Guanine, Adenine, Uracil, Guanine, Cytosine Cytosine Base Pairing A-T (Adenine-Thymine) A-U (Adenine-Uracil) G-C (Guanine-Cytosine) G-C (Guanine-Cytosine) Structure Double helix – made up of two Consists of single chain of spiraling chains of polynucleotides polynucleotides Function Storage and transmission of genetic Transfer of genetic code needed for information the creation of proteins from the nucleus to the ribosome