Unit 1 - Chapter 2 Chemistry of Life

Unit 1 - Chapter 2 Chemistry of Life The Chemical Elements Element- simplest form of matter (containing only one kind of atom) Atom basic unit of structure and function of matter Atomic number the number of protons identifies an atom as a particular element Periodic Table arranges elements by atomic number 91 naturally occurring elements

24 of these elements are important for physiology 6 make up 98.5% of the mass of the human body O, C, H, N, Ca, and P Next 6 make up 0.8% S, K, Na, Cl, Mg, Fe Trace elements 0.7% Cr, Co, Cu, F, I, Mn, Mo, Se, Si, Sn, V, Zn Atomic Structure

Nucleus - center of atom contains protons: positive charge, mass of 1 amu neutrons: neutral charge, mass of 1 amu atomic mass = total # of protons + neutrons Electron shells electrons: negative charge electrons further from nucleus have higher energy Bohr Planetary Model of an Atom

Using the Periodic Table Periodic table Atomic number

represents each element by letter symbols, arranged by atomic number identifies element by number of protons in nucleus Equals the number of protons (P) Atomic mass

Mass of an atom based on the number of protons plus neutrons (P + N) When asked the atomic mass, look up the atomic weight and round to the nearest whole number. (That number is the mass of the most common isotope of the element.)

Atomic weight - average mass of all the isotopes of the element (usually listed on periodic table) Using the Periodic Table Number of Protons = Atomic number Number of Neutrons = Atomic Mass Protons

Number of Electrons = Number of Protons Number of Electrons in the Outer Shell = Number of the Column (Family) the element is in (IA = 1, IIA = 2,etc..) If periodic table uses new numbering system (1-18) then 13 or above just use the ones digit of that number (or subtract 10 from the number of the column) For example Nitrogen = in Column 15, would have 5 electrons in its outershell Determination of Electrons in Each Electron Shell

number of electrons in each shell is limited 2n 2 (n= number of energy level (shell) K shell first (innermost) shell has a maximum of 2 L shell second shell has a maximum of 8 M shell third shell has a maximum of 18

How many electrons in the Outer Shell? Valence electrons are the name for electrons in the outermost shell interact with other atoms determine chemical behavior octet rule - atoms react to obtain a stable number of electrons (8) Never more than 8 in the outer shell even though the shell may be able to hold more than 8 electron, it will never have more than 8 electrons in its outer shell.

Example : Chlorine has 7 in its outer shell. It needs to either gain 1 or lose 7 to have a full outershell (Nature always takes the easy way out - of the two numbers listed above the number that is smaller, is usually the valence number.) How many bonds will an atom form? Depending on the number of electrons in the outer shell, the atom will give up, gain, or share electrons to obtain an electron configuration like the Noble Gases (column 18)

which are the most stable atoms. This means they will usually have 1-4 bonds (although 5 bonds are not unheard of) Example: Sodium has 1 electron in its outer shell. It will either give up 1 (revealing a full 2nd energy level) or gain 7 electrons (making the 3rd energy level have 8 electrons). The easier thing to do would be give up1 electron Therefore 1 bond (dont worry about whether ionic or covalent bonds just be able to determine the number of bonds.) Isotopes and Atomic Weight

Isotopes elements that differ in the number of neutrons 1H, 2H, 3H extra neutrons result in increased atomic weight heavy water have no change in chemical behavior same valence electrons Atomic weight

Average atomic mass of the mixture of isotopes of an element found in a sample Isotopes of Hydrogen ( 1p+, 0n0, 1e- ) ( 1p+, 2n0, 1e- ) ( 1p+, 1n0, 1e- )

Structural Isomers Molecular formulae are identical, but the structures and chemical properties are different Ions Ions - carry a charge, unequal numbers of protons and electrons Ionization - transfer of electrons from one atom to another ( stability of the

valence shell) Anions and Cations Anion - atom gained electron, net negative charge Cation - atom lost an electron, net positive charge Free Radicals A particle with an odd number of electrons superoxide anion O2-. oxygen molecule with an extra electron

Produced by metabolic reactions, radiation, chemicals Causes tissue damage triggers chain reactions that destroys molecules Antioxidants substances that neutralize free radicals SOD (superoxide dismutase enzyme)

vitamin E, carotenoids, vitamin C Chemical Bonds Ionic bonds electrons are given up or gained Covalent bonds electrons are shared Polar bonds share electrons unequally Non-polar bonds share electrons equally Hydrogen bonds no electrons shared, or given up or gained - weak attraction

between molecules Ionic Bonds The attraction of oppositely charged ions to each other forms an ionic bond Ionic bonds are weak and dissociate in water These compounds tend to form crystals... Sodium Chloride Lattice

Covalent Bonds Formed by the sharing of valence electrons Types of covalent bonds single covalent bond double covalent bond nonpolar covalent bond

polar covalent bond Single Covalent Bond One pair of electrons are shared Double covalent bonds: Two pairs of electrons are shared with each C=O bond Nonpolar /Polar Covalent Bonds electrons spend equal

time about each nucleus electrons spend more time about one nucleus Hydrogen Bonds Intermolecular (between molecules) attraction between hydrogen in one molecule and oxygen, nitrogen or fluorine in other molecules. Greatest physiological importance

properties of water shapes of complex molecules proteins, DNA Hydrogen Bonding in Water Inorganic Molecules: Properties of Water Structure polar, V-shaped molecule with 105 bond angle

Solvency Cohesion Adhesion Thermal Stability Chemical reactivity

Solvency Solvency - ability to dissolve matter Water is the universal solvent, important for metabolic reactions and transport of substances Hydrophilic - substances that dissolve easily in water, like sugar, are molecules that have a charge Hydrophobic - substances that do not easily dissolve in water Like Dissolves Like substances that are hydrophilic will be dissolved by hydrophilic solvents (like water.)

Since most substances are at least a little polar, most are a little water soluble. Chemical Reactivity of Water Facilitates and participates in chemical reactions ionization of acids, salts and itself important in the transport of molecules for reactions (universal solvent) involved in hydrolysis and dehydration synthesis Hydrolysis break down molecules by adding water Dehydration Synthesis aka Condensation remove a

molecule of water (producing condensation) to build larger molecules. Acids, Bases and pH An acid is a proton donor A base is a proton acceptor pH measures the concentration of H+ ions in solution pH pH based on the molarity of H+ on a

logarithmic scale pH = -log [H+] Uses the concentration of H+ in moles If [H+] = 100M, 10-1M, 10-2M, etc. Then pH = - log [100] =0, - log [10-1] = 1,-log[10-2] = 2, a change of one number on the pH scale therefore represents a 10 fold change in H+ concentration Chemical Reactions A chemical bond is formed or broken

A chemical equation shows: reactants products Classes of reactions Decomposition reactions Synthesis reactions Exchange reactions Decomposition Reactions Large molecules broken down into simpler ones

AB A + B Starch Glucose molecules Synthesis Reactions Two or more small molecules combine to form a larger one A + B AB

Amino acids Protein molecule Exchange Reactions Two molecules collide and exchange atoms or group of atoms AB+CD ABCD AC + BD Organic Compounds

Summarize the carbohydrates by indicating their chemical composition, types, and some examples and uses. Describe the composition and functions of lipids, including various types of lipids. Identify the chemical makeup, uses, and structures of

proteins. Outline the importance and chemical composition of the nucleic acids, particularly DNA and RNA. Organic Molecules Molecules that contain at least carbon and hydrogen (Carbon dioxide is considered inorganic since it does not contain hydrogen) Carbon bonds readily with other carbon atoms,

hydrogen, oxygen, nitrogen, sulfur needs 4 more valence electrons Can form rings or long carbon chains that serve as the backbone for organic molecules Monomers and Polymers Monomers subunits of macromolecules DNA has 4 different monomers (nucleotides) proteins have 20 different monomers (amino acids)

Polymers series of monomers bonded together Polymerization the bonding of monomers together to form a polymer caused by a reaction called dehydration synthesis Dehydration Synthesis (Condensation) Monomers bond together to form a polymer

(synthesis), with the removal of a water molecule (dehydration) Hydrolysis Splitting a polymer (lysis) by the addition of a water molecule (hydro) Digestion consists of hydrolysis reactions

Functional Groups Groups of atoms attach to carbon backbone Determine the properties of organic molecules Four Macromolecules of living things Carbohydrates (Sugars) Consist of CHO Carbon and Water (hydrogen: oxygen, 2:1)

Lipids (Fats) Consist of CHO Many more hydrogen than oxygen (not a 2:1 ratio) Proteins Consist of CHON (plus Sulfur in some amino acids) Nucleic Acids Consist of CHONP

Organic Molecules: Carbohydrates Hydrophilic organic molecule General formula (CH2O)n , n = number of carbon atoms for glucose, n = 6, so formula is C6H12O6 Names of carbohydrates word root sacchar- or the suffix -ose often used monosaccharide or glucose

Monosaccharides Simplest carbohydrates General formula is C6H12O6 structural isomers Three major monosaccharides glucose, galactose and fructose mainly produced by digestion of complex carbohydrates Disaccharides

Pairs of monosaccharides Three major disaccharides sucrose glucose + fructose lactose glucose + galactose maltose glucose + glucose

Dehydration Synthesis of a Disaccharide Dehydration synthesis of two glucose molecules results in the formation of maltose The C-O-C bond formed is called a glycosidic bond Polysaccharides Starch, cellulose and glycogen long chains of glucose form these polysaccharides

Starch produced by plants is digested by amylase Cellulose gives structure to plants, fiber to our diet Polysaccharides Glycogen is an energy storage polysaccharide produced by animals Liver cells synthesize glycogen after a meal to maintain blood glucose levels Carbohydrate Functions

Source of energy Conjugated carbohydrates glycolipids carbohydrate and lipid moieties Glycoproteins carbohydrate and protein moieties external surface of cell membrane Both serve in cell signaling Address of cell Name badge allows certain substances into cell when the substance binds to a receptor peptidoglycans carbohydrate component dominant

Amino acid crosslinks between the core polysaccharide NAM (N-acyteylmuramic acid) and NAG (N-acetylglucosamine) are the alternating sugars that create the polysaccharide Moieties of Macromolecules A moiety is a chemically different component of a conjugated macromolecule For example, proteoglycans have a protein moiety and a carbohydrate moiety Organic Molecules: Lipids

Hydrophobic organic molecule Less oxidized than carbohydrates, have more calories per gram Five primary types fatty acids

triglycerides phospholipids eicosanoids steroids Fatty Acids Chain of usually 4 to 24 carbon atoms Carboxyl (acid) group on one end and a methyl group on the other

Polymers of two-carbon acetyl groups Fatty Acids Saturated fatty acid - carbon atoms saturated with hydrogen Unsaturated fatty acid - contains C=C bonds that could bond more hydrogen Triglyceride Synthesis (1) Three fatty acids bonded to glycerol by dehydration synthesis

Triglycerides Triglycerides at room temperature Unsaturated fats - liquid called oils, often polyunsaturated fats from plants Saturated fats -solid called fat, saturated fats from animals Function - energy storage also insulation and shock absorption for organs

Phospholipids Amphiphilic character both hydrophobic and hydrophilic regions Hydrophobic tails similar to neutral fats with two fatty acids attached to glycerol Hydrophilic head differs from neutral fat with the third fatty acid replaced with a phosphate group attached to other functional groups A Phospholipid - Lecithin

Steroids Cholesterol other steroids derive from cholesterol cortisol, progesterone, estrogens, testosterone and bile acids required for proper nervous system function and is an important component of cell membranes produced only by animals 85% naturally produced by our body only 15% derived from our diet

Cholesterol All steroids have this 4 ringed structure with variations in the functional groups and location of double bonds Organic Molecules: Proteins Polymer of amino acids 20 amino acids identical except for -R group attached to central carbon amino acid properties

determined by -R group The amino acids in a protein determine its structure and function Amino Acids Nonpolar -R groups are hydrophobic Polar -R groups are hydrophilic

Proteins contain many amino acids and are often amphiphilic Peptides A polymer of 2 or more amino acids Named for the number of amino acids they contain

dipeptides have 2, tripeptides have 3 oligopeptides have fewer than 10 to 15 polypeptides have more than 15 proteins have more than 100 Dehydration synthesis creates a peptide bond that joins amino acids Dipeptide Synthesis

Protein Structure Primary structure determined by amino acid sequence (as the sequence of letters of our alphabet make up different words) Secondary structure helix (coiled), -pleated sheet (folded) shapes held together by hydrogen bonds between nearby groups Tertiary structure

interaction of large segments to each other and surrounding water Quaternary structure two or more separate polypeptide chains interacting Protein Conformation and Denaturation Conformation - overall 3-D shape is crucial to function important property of proteins is the ability to change

their conformation opening and closing of cell membrane pores Denaturation drastic conformational change that destroys the function of a protein as occurs with extreme heat or pH often permanent Shape Dictates Function

Conjugated Proteins Contain a non-amino acid moiety called a prosthetic group Hemoglobin has 4 polypeptide chains, each chain has a complex iron containing ring called a heme moiety Protein Functions Structure Cytoskeletal structure Communication cell receptors

Membrane Transport form channels, carriers (for solute across membranes) Catalysis enzymes are proteins Recognition and protection glycoprotein antigens and antibodies Movement

Flagellar movement Cell Adhesion Cadherin molecules (hold tissues together) Organic Molecules: Nucleotides 3 principle components nitrogenous base single or double carbon-nitrogen ring sugar (monosaccharide)

one or more phosphate groups ATP contains adenine ribose 3 phosphate groups ATP is the universal energy carrying molecule Nucleic Acids DNA (deoxyribonucleic acid)

100 million to 1 billion nucleotides long contains the genetic code for cell division, sexual reproduction, the instructions for protein synthesis RNA (ribonucleic acid) 3 forms of RNA range from 70 to 10,000 nucleotides long carries out instructions given by DNA synthesizes the proteins coded for by DNA

ATP High energy bonds second and third phosphate groups are attached by high energy covalent bonds phosphate groups are negatively charged ATPases hydrolyze the 3rd high energy phosphate bond of ATP releasing energy that can do work in the cell Kinases (phosphokinases)

enzymes that phosphorylate (add the Pi released from ATP to other enzymes or molecules to activate them)

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