Molecular Basis of Life 2024 PDF

Chemical Basis Of Life  Matter The “stuff” of the universe Anything that has mass and occupies space Mass vs. Weight (amount of matter vs. force) States of Matter Solid – has definite shape and volume Liquid – has definite volume, changeable shape Gas –...

Chemical Basis Of Life  Matter The “stuff” of the universe Anything that has mass and occupies space Mass vs. Weight (amount of matter vs. force) States of Matter Solid – has definite shape and volume Liquid – has definite volume, changeable shape Gas – has changeable shape and volume  Composition of Matter Elements – unique substances that cannot be broken down into simpler substances by ordinary chemical means Each element is composed of Atoms Physical and Chemical properties of an element’s atoms give the element its unique properties Atomic symbol – one- or two-letter chemical shorthand for each element  Atomic Structure The Nucleus consists of Neutrons and Protons Neutrons – have no charge (Neutral) and a mass of one atomic mass unit (amu) Protons – have a Positive charge and a mass of one amu Electrons have a negative charge and 1/2000 the mass of a proton (0 amu) Electrons – are located in regions (Orbitals) around the nucleus Atomic Structure: Examples of Different Elements  Major Elements of the Human Body Oxygen (O) – major component of organic and inorganic molecules; as a gas, needed for the production of ATP Carbon (C) – component of all organic molecules – carbohydrates, lipids, proteins, and nucleic acids Hydrogen (H) – component of all organic molecules; as an ion, it influences pH (degree of acidity or alkalinity) of body fluids Nitrogen (N) – component of proteins and nucleic acids Examples of Elements  Lesser and Trace Elements of the Human Body Other Elements Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg), Iodine (I), and Iron (Fe) Trace Elements Required in minute amounts, many are found as parts of enzymes: Selenium (Se), Zinc (Zn), Copper (Cu)  Chemical Composition of the Human Body Oxygen or O – 65% Carbon or C – 18.5% Hydrogen or H – 9.5% Nitrogen or N – 3.2% Calcium or Ca – 1.5% Phosphorous or P – 1.0%  Chemical Constituents of Cells Inorganic Molecules do not contain carbon and hydrogen together, do have other important roles (water, salts, and many acids and bases) Organic Molecules contain carbon covalently bonded to other atoms, determine structure and function  Chemical Constituents of Cells  Common Inorganic Compounds: Oxygen Water Carbon Dioxide (CO2) In Blood: CO2 + H2 + O2 H2CO3 In Lungs: H2CO3 H2O + CO2  Carbon – “living” chemistry depends on C What makes Carbon so special? Carbon (C) has 4 electrons in its outer shell. Because 8 electrons are needed to fill its valence shell, it can form strong, stable covalent bonds with 4 other atoms (usually H, O, N, S, P, or another C).  Carbon can bind to itself, which allows the formation of different carbon-based molecules with unique structures Carbon atoms can form... long chains, branches, and ring structures.  Carbon Bonds Adjacent carbon atoms can also form Double and Triple bonds. carbon-carbon double bond carbon-carbon single bond carbon-carbon triple bond  Organic Molecules – Monomers and Polymers Class Monomer (subunit) Polymer Carbohydrates Sugar Polysaccharides Lipids Fatty Acids Lipids, Phospholipids Proteins Amino Acids Proteins Nucleic Acids Nucleotides (DNA, RNA) Subunits Large Molecules Sugars Polysaccharides Fatty Acids Fats/Lipids/Membranes Amino Acids Proteins Nucleotides Nucleic Acids  Chemical Constituents of Cells Common Organic Substances: Carbohydrates – monosaccharides, disaccharides, & polysaccharides Lipids – saturated & unsaturated fats Proteins – enzymes, antibodies, structural protein (e.g. collagen) Nucleic Acids - nucleotides & polynucleotides  Organic Molecules – Four Classes Lipids Carbohydrates Proteins Nucleic Acids The chemical properties of the different classes depend on the presence of specific functional groups. The larger molecules in each class are formed by joining one or more subunit molecules together.  Organic Molecules – Four Classes Carbohydrates Lipids Proteins Nucleic Acids  Carbohydrates Monosaccharides - simple sugars, single chain or single ring structures Most important in the body are the pentose and hexose sugars Glucose, fructose, and galactose are isomers, they have the same formula (C6H12O6), but the atoms are arranged differently  Carbohydrates Contain carbon, hydrogen, and oxygen, generally the hydrogen to carbon ratio is 2:1 (same as water) carbohydrate – “hydrated carbon” Classified as: Monosaccharide – “one sugar”- exist as straight chains or rings Disaccharide – “two sugars” Polysaccharide – “ many sugars”  Carbohydrates Disaccharides - double sugars – two monosaccharides joined by dehydration synthesis (loss of water molecule) Must be broken down by hydrolysis to simple sugar units for absorption from digestive tract into blood stream  Carbohydrates Polysaccharides - polymers of simple sugars (Polymer – long, chain-like molecule)  Carbohydrates – Types of Polysaccharides Starch - straight chain of glucose molecules, few side branches. Energy storage for plant cells. Glycogen - highly branched polymer of glucose, storage carbohydrate of animals. Cellulose - chain of glucose molecules, structural carbohydrate, primary constituent of plant cell walls. Chitin - polymer of glucose with amino acids attached, primary constituent of exoskeleton  Organic Molecules – Four Classes Carbohydrates Lipids Proteins Nucleic Acids  Answer the following 1. Differentiate organic molecules from inorganic molecule 2. List the 4 classes of organic molecules with its monomer and polymer  Lipids Four Types of Lipids Neutral Fats or Triglycerides Phospholipids Steroids Other Lipoid substances – eicosanoids, lipoproteins  Lipids Lipids are insoluble in water but are soluble in other lipids and in organic solvents (alcohol, ether) or detergents Most of the structure of lipids is non-polar, formed almost exclusively of carbon and hydrogen atoms. Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates  Neutral Fats (Triglycerides or Triacylglyycerols) Glycerol and 3 fatty acids. (Fats & oils) Fatty Acid Glycerol Fatty Acid Fatty Acid  Neutral Fats (Triglycerides or Triacylglyycerols) Commonly known as fats when solid or oils when liquid Composed of three fatty acids (hydrocarbon chains) bonded to a glycerol (sugar alcohol) molecule Neutral Fats (Triglycerides or Triacylglyycerols) Total Fat = 5 grams Saturated Fat = 1 gram What is the rest of the fat? Unsaturated Monounsaturated Polyunsaturated Hydrogenated Cis and Trans fats Neutral Fats (Triglycerides or Triacylglyycerols)  Lipids – Phospholipids Glycerol, 2 fatty acids, 1 phosphate (Cell Membranes) Fatty Acid Glycerol Fatty Acid Phosphate  Phospholipids Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group- main component of cell membranes  Steroids Steroids are fat-soluble with a tetracyclic (four fused carbon rings) base structure. Cholesterol is a constituent of the animal cell membrane and a precursor of other steroids.  Representative Lipids Found in the Body Neutral 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 Fat-soluble vitamins – vitamins A, E, and K Lipoproteins (HDL, LDL) – combinations of fat and protein that transport fatty acids and cholesterol in the bloodstream  Importance of Lipids Long- term Energy storage - highest caloric values per weight Chemical messengers – steroid hormones (testosterone & estrogen) Cell membranes – phospholipids, cholesterol  Organic Molecules – Four Classes Carbohydrates Lipids Proteins Nucleic Acids  Proteins Protein is the basic structural material of the body – 10 to 30% of cell mass Many other vital functions – enzymes, hemoglobin, contractile proteins, collagen, even proteins that help and protect other proteins Most are macromolecules, large (100 to 10,000 a.a.), complex molecules composed of combinations of 20 types of amino acids bound together with peptide bonds  Proteins structural material energy source hormones receptors enzymes antibodies building blocks are amino acids Note: amino acids held together with peptide bonds  Proteins : Amino Acids 20 types of building blocks for protein molecules Each amino acid contains an amine group, a carboxyl group (COOH), and a functional (R) group Differences in the R group make each amino acid chemically unique  Proteins : Amino Acids and Peptide Bonds Proteins are polymers – polypeptides – of amino acids held together by Peptide bonds with the amine end of one amino acid linked to the carboxyl end of the next The order or sequence of the amino acids determine the function of the protein  Structural Levels of Proteins Primary Secondary Tertiary Quaternary  Structural Levels of Proteins Primary – linear sequence of amino acids composing the polypeptide chain (strand of amino acid “beads”)  Structural Levels of Proteins Secondary – alpha helix or beta pleated sheets Both stabilized by hydrogen bonds Hydrogen Bonds in Water Hydrogen Bonds in Protein  Tertiary Hydrogen bonding as well as covalent bonding between atoms in different parts of a polypeptide cause a tertiary structure. It is the tertiary structure that gives a protein its shape and thus determines its function  Quaternary Although some proteins are just polypeptide chains, others have several polypeptide chains and are connected in a fourth level (quarternary).  Structural Levels of Proteins Quaternary – polypeptide chains linked together in a specific manner  Fibrous and Globular Proteins Fibrous proteins (structural proteins) Extended and strandlike proteins Insoluble in water and very stable Examples: keratin, elastin, collagen, and contractile fibers (actin and myosin) Globular proteins (functional proteins) Compact, spherical proteins Insoluble in water and chemically active Examples: antibodies, hormones, and enzymes  Characteristics of Enzymes Most are globular proteins that act as biological catalysts Enzymes are chemically specific Frequently named for the type of reaction they catalyze Enzyme names usually end in –ase (e.g., amylase, protease, nuclease, triose phosphate isomerase, hexokinase) Lower activation energy Characteristics of Enzymes  Mechanism of Enzyme Action Enzyme binds substrate(s) at active site Product is formed at a lower activation energy Product is released  Protein Denaturation The activity of a protein depends on its three-dimensional structure. Intramolecular bonds, especially hydrogen bonds, maintain the structure. Hydrogen bonds may break when the pH drops or the temperature rises above normal  Protein Denaturation A protein is denatured when it unfolds and loses its three-dimensional shape (conformation) Depending upon the severity of the change, Denaturation may be irreversible  Molecular Chaperones (Chaperonins) Help other proteins to achieve their functional three-dimensional shape Maintain folding integrity Assist in translocation of proteins across membranes Promote the breakdown of damaged or denatured proteins heat shock proteins (hsp), stress proteins  Organic Molecules – Four Classes Carbohydrates Lipids Proteins Nucleic Acids  Nucleic Acids – polymers of Nucleotides Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Nucleotides are composed of N-containing base, a pentose sugar, and a phosphate group Five nitrogen bases – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) Two major classes – DNA and RNA  Nucleic Acids – polymers of Nucleotides Nucleotides are composed of N-containing base, a pentose sugar, and a phosphate group Five nitrogen bases – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) Adenine and Guanine Purines – 2-ring structure Cytosine, Thymine, Uracil Pyrimidines – 1-ring structure  1. compare organic & inorganic molecules 2. monomer and polymer of 4 orgNIC MOLECULES.  Structure of DNA Nucleotides are linked by hydrogen bonds between their complementary bases A always bonds to T G always bonds to C Structure of DNA A coiled, double-stranded polymer of nucleotides The molecule is referred To as a double helix Alternating sugar and phosphate? Joined bases?  Deoxyribonucleic Acid (DNA) Double-stranded helical molecule found in the nucleus of the cell (also in mitochondria) Replicates itself before the cell divides, ensuring genetic continuity - it is the genetic material inherited form parents – it is the genetic code Provides instructions for protein synthesis DNA → RNA → Protein Synthesis → Proteins and Enzymes → Structure and Metabolism  Ribonucleic Acid (RNA) Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Sugar is Ribose instead of Deoxyribose Uses the nitrogenous base Uracil instead of Thymine Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA  Adenosine Triphosphate (ATP) Adenine-containing RNA nucleoside with three phosphate groups Source of immediately usable energy for the cell Although glucose is the main cellular fuel, the chemical energy contained in its bonds is not directly used, but the energy released during glucose catabolism is coupled to the synthesis of ATP. From Molecules to Cells  From nonliving chemicals to an organized ensemble that possesses the characteristics of life.  Fundamental unit of life is the cell.  Humans are multicellular organisms  An adult human is composed of about 75 trillion cells. SCALE: 1000 m = 1 mm red blood cell human egg cell white blood cell Smooth muscle cell  Nerve cell – transmits impulses Muscle cells - Epithelial cells – form protective contraction layers