Chemistry Comes Alive.

Name: Chemistry Comes Alive.
Uploaded: 2017-10-04T02:23:44+00:00
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Description: Chemistry Comes Alive.

Chemistry Comes Alive

The Chemistry of Life Atoms, Ions and Molecules Water and Mixtures
Energy and Chemical Reactions Organic compounds

Matter The “stuff” of the universe
Anything that has mass and takes up space States of matter Solid – has definite shape and volume Liquid – has definite volume, changeable shape Gas – has changeable shape and volume

The Chemical Elements Element
simplest form of matter with unique chemical properties Each element has unique physical and chemical properties Physical properties – those detected with our senses Chemical properties – pertain to the way atoms interact with one another

Major Elements of the Human Body
98.5% of body weight consists of Oxygen (O) Carbon (C) Hydrogen (H) Nitrogen (N)

Lesser and Trace Elements of the Human Body
Lesser elements make up 3.9% of the body and include: Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe) Trace elements make up less than 0.01% of the body They are required in minute amounts, and are found as part of enzymes

Periodic Table of the Elements
Atomic number of each element number of protons in its nucleus Periodic table letter symbols of elements arranged by atomic number

Atomic Structure Nucleus - center of atom contains Electron shells
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 # of electrons = # of protons, atoms have neutral charge electrons further from nucleus have higher energy valence electrons are in the outermost shell interact with other atoms determine chemical behavior octet rule - atoms react to obtain a stable number of 8 valence electrons

Bohr Planetary Model of an Atom

Models of Some Elements
p+ represents protons, no represents neutrons

Isotopes and Radioactivity
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 radioisotopes decay to stable isotopes releasing radiation radioisotopes decay to stable isotopes releasing radiation Figure 2.3

Radioisotopes and Radioactivity
same chemical behavior, differ in physical behavior Radioisotopes unstable isotopes Radioactivity radioisotopes decay to stable isotopes releasing radiation Marie Curie

Ionizing Radiation High energy Ejects electrons from atoms
Destroys molecules and produces free radicals sources include: UV light, X rays, nuclear decay (, , )  particle - 2 protons + 2 neutrons can’t penetrate skin  particle - free electron - penetrates skin a few millimeters  particle - high energy, penetrating; very dangerous

Ionizing Radiation 2 Physical half-life Biological half-life
time for 50% of atoms to decay 90Sr - 28 yr. 40K billion years Biological half-life time for 50% of atoms to disappear from the body function of decay and physiological clearance Cesium physical half-life years biological half-life days Radiation exposure background radiation radon gas from decay of uranium in granite cosmic rays

Molecules and Chemical Bonds
two or more atoms of same element covalently bonded Compounds two or more atoms of different elements covalently bonded Molecular formula itemizes each element present and its quantity Structural formula shows arrangement of atoms needed to show structural isomers

Concentration of Solutions
Percent, or parts per 100 parts Molarity, or moles per liter (M) Mole – Avagadro’s number of molecules 6.02 X 1023 A mole of an element or compound is equal to its atomic or molecular weight (sum of atomic weights) in grams

Types of Chemical Bonds
Ionic Covalent Hydrogen

Chemical Bonds Electron shells, or energy levels, surround the nucleus of an atom Bonds are formed using the electrons in the outermost energy level Valence shell – outermost energy level containing chemically active electrons Octet rule – except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their valence shell

Chemically Inert Elements
Inert elements have their outermost energy level fully occupied by electrons Figure 2.4a

Chemically Reactive Elements
Reactive elements do not have their outermost energy level fully occupied by electrons Figure 2.4b

Ions Ions - carry a charge, unequal numbers of protons and electrons
Ionization - transfer of electrons from one atom to another ( stability of valence shell)

Anions and Cations Anion - atom gained electron, net negative charge
Cation - atom lost an electron, net positive charge

Ionic Bonds Attraction of oppositely charged ions to each other forms an ionic bond - no sharing of electrons Ionic bonds are weak and dissociate in water These compounds tend to form crystals...

Formation of an Ionic Bond
Figure 2.5a

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

Polar and Nonpolar Molecules
Electrons shared equally between atoms produce nonpolar molecules Unequal sharing of electrons produces polar molecules Atoms with six or seven valence shell electrons are electronegative Atoms with one or two valence shell electrons are electropositive

Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds
Figure 2.8

Hydrogen Bonds Weakest of the bonds
Attraction between polar molecules – no sharing of electrons Greatest physiological importance properties of water shapes of complex molecules proteins, DNA

Hydrogen Bonding in Water

Adhesion and Cohesion Adhesion - attraction between one substance and another substance Cohesion - attraction between one substance and itself water is very cohesive due to hydrogen bonds Surface tension elastic surface film caused by the attraction of molecules at the surface from those below

Thermal Stability of Water
Heat capacity: amount of heat required to raise the temperature of 1g of a substance by 1°C Calorie: amount of heat required to raise the temperature of 1g of water by 1°C Water stabilizes internal temperature of the body high heat capacity its hydrogen bonds inhibit increased temperature (molecular motion) caused by increased heat effective coolant 1 ml of perspiration removes 500 calories from the body

Properties of Water Reactivity – is an important part of hydrolysis and dehydration synthesis reactions Cushioning – resilient cushion around certain body organs InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids PLAY

Mixtures and Solutions
Mixtures – two or more components physically intermixed (not chemically bonded) Solutions – homogeneous mixtures of components Solvent – substance present in greatest amount Solute – substance(s) present in smaller amounts

Solvency Solvency - ability to dissolve matter
Hydrophilic - charged substances that dissolve easily in water Hydrophobic - neutral substances that do not easily dissolve in water Water is the universal solvent, important for metabolic reactions and transport of substances

Water as a Solvent Water molecules overpower the ionic bond above between Na+Cl- by forming hydration spheres. Note orientation of water molecules: negative pole faces Na+, positive pole faces Cl-

Mixtures Substances that are physically blended but not chemically combined Solutions Colloids Suspensions

Solutions Solute < 1nm Transparent e.g. copper sulfate solution
pass through membranes Transparent e.g. copper sulfate solution

Colloids Particles 1 to 100nm Cloudy e.g. milk protein
to large to pass through membranes Cloudy e.g. milk protein

Suspensions Particles >100nm Cloudy or opaque Separate on standing
e.g. blood cells

Measures of Concentration
Weight per Volume weight of solute in a given volume of solution e.g. IV saline contains 8.5 g/L NaCl Percentages weight or volume of solute in solution e.g. IV D5W (5% w/v dextrose in distilled water) 5 grams of dextrose in add 100ml water Molarity number of moles of solute/liter in solution physiologic effects of a chemical based on the number of molecules in solution

Salts Inorganic compounds
Contain cations other than H+ and anions other than OH– Are electrolytes; they conduct electrical currents

Acids and Bases Acids release H+ and are therefore proton donors
HCl  H+ + Cl – Bases release OH– and are proton acceptors NaOH  Na+ + OH–

Acid-Base Concentration (pH)
Acidic solutions have higher H+ concentration and therefore a lower pH Alkaline solutions have lower H+ concentration and therefore a higher pH Neutral solutions have equal H+ and OH– concentrations

pH pH - based on the molarity of H+ on a logarithmic scale
pH = -log [H+] for molarity of H+ = 100,10-1,10-2,etc. pH = - log [100] = 0, - log [10-1] = 1, etc. a change of one number on the pH scale therefore represents a 10 fold change in H+ concentration Our body uses buffers to resist any change in pH

pH Scale

Buffers Systems that resist abrupt and large swings in the pH of body fluids Carbonic acid-bicarbonate system Carbonic acid dissociates, reversibly releasing bicarbonate ions and protons The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Acid/Base Homeostasis PLAY

Work and Energy Energy - the capacity to do work
Kinetic energy - energy of motion Potential energy- inherent energy due to an objects position or internal state Chemical energy - potential energy stored in the molecular bonds Electromagnetic energy - kinetic energy of photons: light, infrared, UV, X rays +  rays

Chemical Reactions Occur when chemical bonds are formed, rearranged, or broken Are written in symbolic form using chemical equations Chemical equations contain: Number and type of reacting substances, and products produced Relative amounts of reactants and products

Examples of Chemical Reactions

Patterns of Chemical Reactions
Combination reactions: Synthesis reactions which always involve bond formation A + B  AB Decomposition reactions: Molecules are broken down into smaller molecules AB  A + B Exchange reactions: Bonds are both made and broken AB + C  AC + B

Energy Flow in Chemical Reactions
Exergonic reactions – reactions that release energy Endergonic reactions – reactions whose products contain more potential energy than did its reactants

Metabolism All the chemical reactions of the body Catabolism Anabolism
energy releasing (exergonic) decomposition reactions Anabolism energy releasing (endergonic) synthesis reactions

Reaction Rates Basis for chemical reactions is molecular motion and collisions Reaction Rates affected by: concentration more concentrated, more collisions, faster rx temperature higher temperature, greater collision force, faster rx catalysts speed up reactions without permanent change to itself biological catalysts are enzymes

Oxidation-Reduction (Redox) Reactions
Reactants losing electrons are electron donors and are oxidized Reactants taking up electrons are electron acceptors and become reduced

Energy Flow in Chemical Reactions
Exergonic reactions – reactions that release energy Endergonic reactions – reactions whose products contain more potential energy than did its reactants

Organic Compounds Molecules unique to living systems contain carbon and hence are organic compounds They include: Carbohydrates Lipids Proteins Nucleic Acids

Organic Molecules: 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

Functional Groups Groups of atoms attach to carbon backbone
Determine the properties of organic molecules

Monomers and Polymers Monomers Polymers Polymerization
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

Hydrolysis Splitting a polymer (lysis) by the addition of a water molecule (hydro) Digestion consists of hydrolysis reactions

Carbohydrates Contain carbon, hydrogen, and oxygen
Their major function is to supply a source of cellular food Examples: Monosaccharides or simple sugars Figure 2.13a

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 Three major 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

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 external surface of cell membrane glycoproteins mucus of respiratory and digestive tracts proteoglycans carbohydrate component dominant cell adhesion, gelatinous filler of tissues (eye) and lubricates joints

Lipids Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates Examples: Neutral fats or triglycerides Phospholipids Steroids Eicosanoids

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 (2)
Triglycerides called neutral fats fatty acids bond with their carboxyl ends, therefore no longer acidic

Triglycerides Hydrolysis of fats occurs by lipase enzyme
Triglycerides at room temperature liquid called oils, often polyunsaturated fats from plants solid called fat, saturated fats from animals Function - energy storage also insulation and shock absorption for organs

Phospholipids Amphiphilic character
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

Eicosanoids Derived from arachidonic acid (a fatty acid)
Function as chemical signals between cells Includes prostaglandins role in inflammation, blood clotting, hormone action, labor contractions, control of blood vessel diameter

Cholesterol All steroids have this 4 ringed structure with variations in the functional groups and location of double bonds

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 Eicosanoids – prostaglandins, leukotriens, and thromboxanes Lipoproteins – transport fatty acids and cholesterol in the bloodstream

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 Building blocks of protein, containing an amino group and a carboxyl group Amino acid structure InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids PLAY

Amino Acids Figure 2.15a-c

Amino Acids Figure 2.15d, e

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 Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.16

Structural Levels of Proteins
Primary – amino acid sequence Secondary – alpha helices or beta pleated sheets Chemistry of Life: Proteins: Secondary Structure PLAY

Structural Levels of Proteins
Tertiary – superimposed folding of secondary structures Quaternary – polypeptide chains linked together in a specific manner Chemistry of Life: Proteins: Tertiary Structure PLAY Chemistry of Life: Proteins: Quaternary Structure PLAY

Fibrous and Globular Proteins
Fibrous proteins Extended and strandlike proteins Examples: keratin, elastin, collagen, and certain contractile fibers Globular proteins Compact, spherical proteins with tertiary and quaternary structures Examples: antibodies, hormones, and enzymes

Protein Denuaturation
Reversible unfolding of proteins due to drops in pH and/or increased temperature Figure 2.18a

Protein Denuaturation
Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes Figure 2.18b

Characteristics of Enzymes
Most are globular proteins that act as biological catalysts Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion) Enzymes are chemically specific Frequently named for the type of reaction they catalyze Enzyme names usually end in -ase Lower activation energy

Characteristics of Enzymes
Figure 2.19

Mechanism of Enzyme Action
Enzyme binds with substrate Product is formed at a lower activation energy Product is released PLAY How Enzymes Work

Nucleic Acids (C), thymine (T), and uracil (U) Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine Two major classes – DNA and RNA

Deoxyribonucleic Acid (DNA)
Double-stranded helical molecule found in the nucleus of the cell Replicates itself before the cell divides, ensuring genetic continuity Provides instructions for protein synthesis

Structure of DNA Figure 2.21a

Structure of DNA Figure 2.21b

Ribonucleic Acid (RNA)
Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Uses the nitrogenous base uracil instead of thymine Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA

Adenosine Triphosphate (ATP)
Source of immediately usable energy for the cell Adenine-containing RNA nucleotide with three phosphate groups

Adenosine Triphosphate (ATP)
Figure 2.22

How ATP Drives Cellular Work
Figure 2.23

Chemistry Comes Alive.

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