CHAPTER 2: Chemical Principles




Isotopes – atoms with different
numbers of neutrons in their nuclei
Atom – the smallest component of a

Have the same number of protons
pure substance that exhibits physical and

Atomic weight differ because of the
chemical properties of that substance
difference in the number of neutrons

Cannot be subdivided into smaller
 Electron Shells – regions
substances without losing its properties

Smallest units of matter that enter
into chemical reactions

Atoms interact with each other in
certain combinations to form molecules
corresponding to different
Chemistry – the science of the
energy levels
interaction between atoms and molecules
 The arrangement is called

Every atom has a centrally located
electronic configuration
nucleus (bears a net positive charge)
How Atoms Form Molecules : Chemical
and particles called electrons that move
Bonds
around the nucleus in regions called
electron shells
 Valence – or combining capacity,
of an atom is the number of extra
Protons – positively (+) charged
or missing electrons in its
particles
outermost electron shell
Neutrons – uncharged (neutral)
particles
 Compound – a molecule that
Electrons – negatively (-) charged
contains at least two different
particles
kinds of atoms such as H2O
Charge – a property of some
 Chemical Bonds – molecules
subatomic particles that produces an
hold together because the
attractive or repulsive force between them
valence electrons of the

Particles of opposite charge attract
combining atoms form attractive
each other
forces between the atomic nuclei

Particles of the same charge repel
 2 ways for atoms to form
each other
bonds:
 Gaining/losing electrons
Atomic Number – the number of
from their outer electron
protons in the nucleus
Atomic Weight – the total number of
shell
 Sharing outer electrons
protons and neutrons in an atom
Na –Latin name, natrium – to
distinguish it from N and S

92 naturally occurring elements

26 elements commonly found in living
organisms

 Ionic Bond – when atoms gained
or lost outer electrons
 Covalent Bond – when outer
electrons are shared
Ionic Bonds

energy is immune system (antibodies) combine with directed inward foreign substances (antigens) to combat  Exergonic reaction (exo=out) infection – a chemical reaction that   Cations .in which hydrogen atom that is covalently bonded to one oxygen or nitrogen atom is attracted to another oxygen or nitrogen atom  Such bonds are weak & do not bind atoms into molecules  Serves as bridges releases more energy than it absorb. ions. or molecules combine to form new and larger molecules  Forms new bonds A+B AB  A .product  Arrow . B – reactant  AB .indicates the direction in which the reaction proceeds  Anabolic reaction / anabolism – pathways of synthesis reactions in living organisms .an attraction Chemical reactions – involve the between ions of opposite charge that holds them together to formmaking or breaking of bonds between atoms a stable molecule Chemical energy – occurs when  An attraction between bonds between atoms are formed or broken atoms in which one atom during chemical reactions loses electrons and another atom gains electrons Endergonic reaction  Antigen-Antibody reactions – (endo=within) – a chemical reaction that reactions in which molecules produced by theabsorb more energy than it releases.positively charged ions Anions – negatively charged ions Covalent Bonds  Covalent Bond – a chemical bond formed by two atoms sharing one or more pairs of electrons  Single covalent bond – 1 pair of electrons formed  Double covalent bond – 2 pair of electrons formed  Triple covalent bond – 3 pair of electrons formed Hydrogen Bonds  Hydrogen Bond . energy is directed outward 3 Basic Types of Chemical Reaction common to living cells  Synthesis reaction – when two or more atoms. Ion – negatively or positively charged atom  Electron Donor – gaining electrons  Electron Acceptor – losing electrons Molecular Weight and Moles Molecular weight – the sum of the atomic weights of all its atoms Mole – unit .of a substance is its molecular weight expressed in grams Chemical Reactions  Ionic Bond .

Celsius (boiling point) reactions that occur in living Excellent dissolving medium or organisms solvent Reactant or product in many chemical  Exchange reactions – actually reactions part of synthesis and part of Key reactant in the digestive decomposition processes of organisms Also involved in synthetic reactions Strong hydrogen bonding between water molecules makes water an excellent temperature buffer AB B A+ AB + CD + BC AD Polar molecule – having unequal distribution of charges The reversibility of Chemical Reactions Acids. bases)  Organic compounds – always contain carbon and hydrogen and typically are structurally complex  Base – dissociates into one or more positive ions plus one or more negatively charged hydroxide ions (OH-) that can accept or combine with protons  Salt – a substance that dissociates in water into cations and anions. salts. Bases. CO2.decomposition molecules 100 deg. and Salts Ionization / Dissociation – break  Reversible reaction – a chemical apart into ions reaction that is readily reversible. usually small and structurally simple. indicated by Acid – a substance that dissociates two arrows into one or more hydrogen ions ( H+) and one or more negative ions Proton donor (H+) Important Biological Molecules A+B AB  Inorganic compounds – molecules. which typically lack carbon and in which inorganic bonds may play an important role (O2. Decomposition reaction – reverse of a synthesis  To decompose means to break down into smaller parts  Bonds are broken Macromolecules – giant molecules Inorganic Compounds Water One of the most abundant Every water molecule is capable of forming hydrogen bonds with nearby water molecules Strong attraction between water  Catabolic reaction / catabolism . neither of H+ or OH- . acids.

potential of hydrogen. ranges Alcohol (-OH) – hydrophilic and thus from 0 – 14 attracts water molecules to it. building block of deoxyribonucleic acid (DNA).chain of carbon atoms in an organic molecule Simple carbohydrates – used in the synthesis of amino acids and fats or fatlike . P  Carbon skeleton . the H. This calculation for a solutions pH : -log10 [H+] attraction helps dissolve organic molecules Acidic containing hydroxyl groups  More H+ Carboxyl group (-COOH) – source of  pH lower than 7 hydrogen ions. specific group of atoms that are most sensitive to even small changescommonly in the involved in chemical reactions and acidity or alkalinity of the environments are responsible for most of the characteristic in which they occur chemical properties of a particular organic   compound  pH . N molecule that carries hereditary information  Less often are S.Acid-Base Balance : The Concept of pH Bonding of other elements with carbon  Biochemical reactions – chemical and hydrogen forms characteristic functional reactions in living systems . do well R – remainder of the molecule ( R-OH) in alkaline habitats Macromolecules . pH water is released from 1-3. extremely groups.5  Sulfuric acid produced from this Carbohydrates bacterium in mine water is important in dissolving uranium and copper from Are a large and diverse group of low-grade ore organic compounds that includes sugars Organic Compounds and starches  Common elements that attach to C are Deoxyribose – sugar. has its natural environment human skin. tends bonding of many repeating small to be slightly acidic.very large  Propionibacterium acnes – amolecules  Polymers – formed by covalent bacterium that causes acne. pH of about 4 molecules called monomers  Thiobacillus ferrooxidans – a bacterium that metabolizes elemental Dehydration synthesis / Condensation reaction – a molecule of sulfur and produces sulfuric acid. molecules containing it have  Basic acidic properties  More OHAmino group (-NH2) – functions as bases because they readily accept hydrogen  pH buffers – compounds that help ions keep the pH from changing drastically Sulfhydryl group (-SH) – helps  Fungi – best able to tolerate acidic stabilize the intricate structure of many proteins conditions  Cyanobacteria – prokaryotes. O.

main energy-supplying molecule  Essential to the structure and function of living cells of membranes that separate living cells from their environment Disaccharides – 2  Has C. H. tetroses. main Formula is (CH2O)n component of the cell walls of plants and most algae 3 Major Groups Based on Size  Dextran – produced as a sugary slime Monosaccharides – simple by certain bacteria. etc.substances. H.) glucose molecules in glycogen.  Amylase – break bonds between the pentoses.two molecules with  energy storage the same chemical formula but . and O atoms sugars Ratio of H to O is 2:1  Not usually soluble in water  Ribose (C5H10O5)  Glycogen –composed of glucose  Glucose (C6H12O6) subunits and is synthesized as a storage  Sucrose (C12H22O11) material by animals and some bacteria  Cellulose – glucose polymer. carbohydrates . but lack the monosaccharides bond in a 2:1 ratio of H and O atoms dehydration synthesis reaction  Nonpolar molecules. and insects molecules of simple sugars is  Starch – polymer of glucose produced indicated by the prefix in its by plants and used as food by humans name (trioses. and O atoms. reverse of dehydration synthesis Function of carbohydrates is Polysaccharides – consist of tens or mainly to fuel cell activities with hundreds a of monosaccharides joined through ready source of energy dehydration synthesis  Lack the characteristic sweetness of Made up of C. which are used to build cell membranes and other structures                different structures and properties  Hydration – disaccharides can Macromolecular be broken down into smaller. used in a blood sugars plasma substitute Each molecules has 3-7 carbon  Chitin – makes up part of the cell wall atoms of most fungi and exoskeletons of # of carbon atoms in the lobsters. crabs. but Pentoses and Hexoses – cannot break the bond in cellulose important to living organisms  Cellulase – can digest cellulose DNA –has pentose Lipids Glucose – common hexose. no positive or Disaccharide sucrose(table negative end (pole) sugar) – glucose + fructose  insoluble in water. but dissolves easily Disaccharide lactose (milk in nonpolar solvents sugar)– glucose + galactose  provide structure of membranes Isomers .functions as simpler molecules when water is food reserves added.

because they relatively straight also found in fungi and plants  Separate the fatty acid chains and and able to pack together more closely than unsaturated chains thus prevent the packing that would Unsaturated – the double bonds harden the plasma membrane at low create kinks in the chain. O Transport proteins – help transport  Phospholipids – made up of certain chemicals into and out of cells glycerol. H. becomes solid more easily group of bacteria (mycoplasmas). steroid the carbon skeleton contains the  Important constituent of the plasma maximum number of hydrogen membranes of animal cells and of one atoms. same side O. N. triglyceride  Ester linkage – the chemical bond formed where the water molecule is removed        polar (phosphate group & glycerol) & nonpolar regions (fatty acids) Mycobacterium tuberculosis – a bacterium that causes tuberculosis. some also contain S Trans fatty acid – H atoms on  Essential ingredients in all aspects of opposite sides of the double bond cell structure and function  Complex lipids – contains Enzymes – are proteins that speed up elements such as P. Simple Lipids – fats or triglycerides contain an alcohol called glycerol and group of compounds known as fatty acids   A molecule of fat is formed when a molecule of glycerol combines with 1-3 fatty acid molecules Based on # of fatty acids : monoglyceride. N . kill other bacteria phosphate group bonded to one Exotoxins – produced by some or several organic groups disease-causing microorganisms  builds membranes Hormones – regulatory functions  essential to a cells survival . is distinguish by its lipid-rich content  Cell wall contains complex lipids such as waxes and glycolipids(lipids w/ carbohydrates attached) that gives the bacterium distinctive staining characteristics Steroids – structure of steroid cholesterol with four interconnected carbon Primary function of lipids is to rings that are characteristic of steroid from plasma membranes that  Sterol – when an –OH group is enclose cells attached to one of the rings of the Saturated .no double bonds. and in Bacteriocins – produced by many place of a third fatty acid is a bacteria. S in biochemical reactions addition to C. which temperatures keep the chains apart from one Proteins another Cis fatty acid –H atoms on the  Organic molecules that contain C. H. 2 fatty acids. diglyceride.

which is the amino acids distinguishing feature Tyrosine – an amino acid that has a cyclic side group  Stereoisomers – has two configurations : D and L . it may unravel and lose form from roughly its characteristic shape . also attached is a side group (R group). 3D shapes  D – right handed  L – left handed  Peptide Bonds  Peptide bonds – bonds between amino acids  Dipeptide .2 amino acids joined by a peptide bond  Tripeptide – 3 amino acids  Peptide – 4-9 amino acids  Polypeptide – 10-2000 or more amino acids Levels of Protein Structure  Hydrogen bonding between O or N atoms that are part of the polypeptide’s backbone  Tertiary structure – overall 3D structure of a polypeptide chain  Folding is not repetitive or predictable  Involves several interactions between various amino acid side groups in the polypeptide chain  Hydrophobic interaction – helps contribute to tertiary structure  H bonds between side groups & ionic bonds between oppositely charged side groups. pH. also contribute to tertiary structure Disulfide bridges – proteins that contain the amino acid cysteine form strong covalent bonds  Contains (-SH) sulfhydryl groups and S of one cysteine molecule bonds with another S of the other (S-S) by removal of H atoms Quaternary Structures – consist of  Primary structure – amino an aggregation of 2 or more individual polypeptide chains that operate as a single acids are linked together to functional unit from a polypeptide chain  Globular shape – compact and  Secondary structure – roughly spherical repetitious twisting or folding of  Fibrous shape – threadlike the polypeptide chain  Denaturation – when a protein  Helices –clockwise encounters a hostile environment in spirals terms of temperature.  Antibodies.play a role in vertebrate immune systems Amino Acids   Building blocks of proteins Attached to its alpha-carbon id at least 1 carboxyl group (-COOH) and 1 amino group (-NH2) = alpha-amino acids.which concentrations. protein is no parallel portions of the longer functional chain . or salt  Pleated sheets .

O)  Adenine (A) ATP  Thymine (T)  Cystosine (C ) Adenosine triphosphate – principal  Gunaine (G) energy-carrying molecule of all cells and is  Uracil (U) indispensable to the life of the cell  A & G.Simple proteins – contains only amino acids  Conjugated proteins – combination of amino acids with other organic or inorganic components  Named by their non-amino acid component  Glycoproteins .double-ring  Stores chemical energy released by structures called purines chemical reactions  T. no phosphate group DNA     Consists of two long strands wrapped around each other to from a double helix A & T – held by 2 H bonds G & C – by 3 H bonds No Uracil  Complementary – when the sequence of bases of one strand is determined by the sequence of bases of the other RNA    Single-stranded Pentose sugar is a ribose – which has 1 more Oxygen atom than deoxyribose RNA’s bases is URACIL (U) instead of Thymine  Messenger RNA (mRNA)  Ribosomal RNA (rRNA)  Transfer RNA (tRNA)  Nucleotides . important regulators of activity in eukaryotic cells  Nucleic Acids Oswald Avery. U – single-ring  Provides energy for reactions that structures called require energy pyrimidines . Colin MacLeod. H.has sugars  Nucleoproteins – has nucleic acids  Metalloproteins – has metal atoms  Lipoproteins – has lipids  Phosphoproteins – has phosphate groups. C. N. Maclyn McCarty (1944) – discovered DNA the substance which genes are made  James Watson & Francis Crick – work with molecular models and X-ray information  Maurice Wilkins & Rosalind Franklin – identified the physical structure of DNA   Nucleic acids – DNA & RNA discovered in the nuclei of cells.3 parts:  Nitrogen-containing base (cyclic compounds that has C. nucleotides structural unit and named according to their nitrogen-containing base  Pentose sugar (deoxyribose or ribose) Phosphate group (phosphoric acid)   Nucleoside – combination of purine or pyrimidine + pentose sugar.

 Adenosine unit – adenine & ribose w/ 3  phosphate group attached. in other words (adenine nucleotide or adenine monophosphate or AMP) w/ 2 extra phosphate groups Releases large amount of energy when the 3rd phosphate group is hydrolyzed into ADP .