Organic Chemistry - St. Johns County School District

Organic Chemistry Chapters 22 Hydrocarbons Chapter 22 O-Chem Chemists knew that living organisms were made up of an obscene number of carbon compounds and thus referred to them as organic Organic Compound: the term applied to any and all chemical compounds that contain carbon with the only exceptions being carbon oxides, carbides and carbonates (these are inorganic) Why study nothing but carbon for an entire life and centuries? Remember that it is in Group 14 and thus has four valence electrons Therefore, it can make four bonds to complete is stable valence octet Carbon atoms bond with numerous different atoms, including itself! Catenation: the covalent binding of an element to itself to form chains or rings

Hydrocarbons The simplest organic compounds are known as hydrocarbons These contain only carbon and hydrogen If you think that only a few could be made, think again Thousands of different hydrocarbons exist! Carbon will form four covalent bonds while hydrogen will form only one So the simplest organic hydrocarbon compound is CH4 Carbon tetrahydride METHANE! A Review of Models Chemist represent molecules in a variety of ways They will use molecular formulas but these lack the geometric shape that molecules form A structural formula shows the general arrangement of atoms but again, not the exact geometry of the bonds/atoms

Space-filling models give a more realistic picture of what a molecule would look like but the ball-and-stick models give the best geometric shape Straight-Chain Alkanes Methane is the smallest member of a series of hydrocarbons known as alkanes Alkanes: hydrocarbons that have only single bonds between atoms Name Molecula r Formula Structural Formula Isomer s Name Molecula r Formula Structural Formula

Isomers methan e CH4 CH4 1 hexane C6H14 CH3(CH2)4CH3 5 ethane C2H6 CH3CH3 1 heptane C7H16

CH3(CH2)5CH3 9 propane C3H8 CH3CH2CH3 1 octane C8H18 CH3(CH2)6CH3 18 butane C4H10 CH3CH2CH2CH3 2 nonane C9H20

CH3(CH2)7CH3 35 pentane C5H12 CH3(CH2)3CH3 3 decane C10H22 CH3(CH2)8CH3 75 These compounds are known as a homologous series because they differ from one another by a repeating unit (number of C and H) Isomers Compounds that have the same molecular formula but have different structures Structural Isomers: constitutional isomers are isomers where the atoms are bonded together in

different orders These have different physical and chemical properties H H C H H H H H H H H H H H Methane CH4 Butane C4H10 H ? R C H H Methyl -CH3 C C C C H

H H H H R C C C C H H H H H Butyl -C4H9 Isomers Geometric Isomers: Isomers in which the order of the atom bonding is the same but the arrangement of atoms in space is different Branched-Chain Alkanes The first set of alkanes were straight and without side chains Branched-chain alkanes will have one chain that is longer than others This chain, the longest-continuous chain of carbon atoms is called the parent chain All side chains (branches) are called substituent

groups because they appear to substitute for a hydrogen atom in the straight chain Be sure to get and keep a copy of your quick reference guide for naming alkanes Branched-Chain Nomenclature Similar to naming compounds and molecules, you will use the IUPAC Nomenclature Rules 1. 2. International Union of Pure and Applied Chemistry Count the number of carbon atoms in the longest continuous chain. Use the name of the straight-chain alkane to name the parent chain Number each carbon in the parent chain a. Locate the end carbon closest to a substituent group i. 3. 4.

Name each alkyl group substituent. The names of the groups are placed before the name of the parent chain If the same alkyl group occurs more than once as a branch on the parent structure, use a prefix (di, tri, tetra, etc.) before its name to indicate how many times it appears a. 5. 6. Label that carbon position one (This gives all substituent groups the lowest possible number) Then use the number of the carbon to which each is attached to indicate its position Whenever different alkyl groups are attached to the same parent structure, place their names in alphabetical order (prefixes are not included in alphabetical order) Write the entire name using hyphens to separate numbers from words and commas to separate numbers a. No space is added between the substituent name and the name of the parent chain Naming Branched Alkanes (IUPAC) Octane 4-ethyl 6

8 5 7 2 4 3 4-ethyl-3,5-dimethyloctane 1 3-methyl and 5-methyl = 3,5-dimethyl 1. Root name: name of longest continuous C chain (parent chain) Two equally long? Choose the one with more branches 2. Number C atoms in chain, starting at end with first branch 3. Identify substituents, give each a number (C it is connected to) Two or more identical substituents: use prefixes (di-, tri-, tetra-, etc.) 4. List substituents alphabetically before root name Do not alphabetize prefixes 5. Punctuation: commas separate numbers from each other hyphens separate numbers from names no space between last substituent & root name

Structural Isomers: Pentane (C5H12) pentane 2-methylbutane 2,2-dimethylpropane Structural Isomers: Hexane (C6H14) hexane 2,3-dimethylbutane 2-methylpentane 2,2-dimethylbutane 3-methylpentane Structural Isomers: Heptane (C7H16) heptane 2,2-dimethylpentane 2-methylhexane 2,3-dimethylpentane 3-methylhexane Structural Isomers: Heptane C7H16 2,4-dimethylpentane 3-ethylpentane 3,3-dimethylpentane

2,2,3-trimethylbutane Cyclic Alkanes One reason that there are thousands of carbon compounds is because they dont always form straight/branched-chains They can form circles or rings Cyclic hydrocarbons Cycloalkanes are hydrocarbons that contain only single covalent bonds Naming these rings involves added the prefix cyclo- before the carbon chain Cyclopropane, cyclohexane, etc. Naming Substituted Cycloalkanes Like other alkanes, cycloalkanes can also have substitute chains (groups) They follow the same IUPAC Nomenclature except for a few subtle

differences 1. 2. There is no longest chain because the parent chain is the ring itself Because there is no beginning or end in a cyclo, the numbering is started on the carbon that is bonded to the substituent group a. If there are two or more substituent groups, use the combination of numbers that give the lowest possible set Multiple Covalent Bonds Recall that carbon can also make multiple covalent bonds (2 or 3) If a carbon compound (organic) contains only single covalent bonds, its said to be a saturated hydrocarbon If just one of the carbons in the organic compound contains a double or triple bond, then it will be unsaturated Saturated means that its loaded with the maximum number of atoms because its using all of its bonds for only one other atom

Alkenes Unsaturated hydrocarbons that contain at least one double covalent bond is known as an alkene Alkenes are named in much the same way as alkanes but their suffix will be an ene instead of ane Ethane : ethene, propane : propene To name alkenes with four or more carbons, one must first locate the double bond Numbering of the carbons in the parent chain must start at the end that will give the first carbon in the double bond the lowest number Use only that number in the name The same is true for cycloalkenes Branched-Chain Alkenes The same branched-chain IUPAC nomenclature is true for these unsaturated hydrocarbons with only two small differences

The parent chain is always the longest chain that contains the double bond, whether or not its the longest chain of carbon atoms The position of the double bond, not the branches, determines how the chain is numbered If there are multiple double bonds, then a prefix must be used before the suffix (diene, triene, tetraene) This again will require the carbon atoms to have the lowest number assignments Cis- vs. Trans- Alkynes A carbon compound that contains at least one triple bond will be known as an alkyne These unsaturated hydrocarbons will use all the same nomenclature rules as alkenes except the suffix will be changed to yne Aliphatic Hydrocarbons Alkane

General formula Typical structural formula Carbon-carbon bond type Naming suffix Alkene Alkyne Alkadiene CnH2n + 2 CnH2n CnH2n - 2 CCCC C=CCC C =CCC C=CC=C butane

1-butene 1-butyne 1,3-butadiene all single bonds one double bond one triple bond two double bonds -ane -ene -yne -diene CnH2n - 2 Benzene An Aromatic Compound C6H6

Resonance structures Shorthand notation of Benzene Structure of Benzene H H C C C H H C C H C H Structure of Benzene H H C C C H H C

C H C H Structure of Benzene H H C C C H H C C H C H Benzene 3-D VSEPR Diagram Substituted Hydrocarbons & Their Reactions Functional Groups

Functional Groups An atom or group of atoms that is responsible for the specific properties of an organic compound The same functional group will undergo the same chemical reactions no matter the parent chain Therefore, compounds that contain the same functional group can be classified together Functional Groups Alcohols An organic compound that contains one or more hydroxyl groups General form is R OH Name of alcohols will end in ol Or hydroxy- Hydrogen bonding is possible in alcohols Used today as alternative fuel sources

Alkyl Halides An organic compound that contains one or more halogen atoms General form is R X Called either Element-chain or chain element Bromoethane or Ethyl bromide Some of the most commonly used organic compounds CFCs were used in refrigerants and caused the destruction of the ozone layer years ago Banned by most countries One single chlorine atom can destroy thousand of ozone molecules, O3 Ethers An organic compound in which two hydrocarbon groups are bonded together by the same single oxygen atom

General form is R O R Named Chain-oxy-chain R can be the same hydrocarbon group as the other They are not very reactive so they are used in solvents Aldehydes and Ketones Aldehydes are compounds that contain a carbon that is bonded to a hydrogen and double-bonded to an oxygen These will be found on the end of the chain These are known as carbonyl groups Named as you would an alcohol but with al ending Ketones are similar to ethers and aldehydes both but differ because two hydrocarbon groups are attached by a single carbon, which is double-bonded to an oxygen atom These end in one when naming Aldehydes

and Ketones Acetaldehyde ethanal, ethyl aldehyde O (CH3CH) Formaldehyde methanal (CH2O) Aldehyde Ketone O R-C-H O R-C-R' Acetone dimethyl ketone, 2-propanone (CH3COCH3) Amines An organic compound in which a nitrogen atom connects a hydrocarbon group with multiple different other atoms Named as either amino- or -amine This could include other hydrocarbons Thought to be derived from ammonia, NH3

R can be the same hydrocarbon group as the other They are not very reactive so they are used in solvents Carboxylic Acids An organic compound that contain the carboxyl group These are acids or proton donors! It is a weaker acid as compared to those in inorganic compounds Can be found in citrus fruits (citric acid) Named oic acid Esters An organic compound similar to carboxylic acid except the hydrogen atom has been replaced by an alkyl group Considered derivatives of carboxylic acids

Common locations are found in the backbone of our DNA Explosives Named alkyl alkanoate Functional Groups Order of Priority of Functional Groups Order of priority Functional group Formula 1 Carboxylic acid 2 -COOH Order of priority Functional group Formula

8 Ketone -CO Sulfonic acid -SO3H 9 Alcohol -OH 3 Ester 10 Phenol -OH 4 Acid chloride -COCl 11 Thiol

5 Amide -CONH2 12 Amine -NH2 6 Nitrile -CN 13 Ether -OR 7 Aldehyde -CHO 14

Sulfide -SR -COOR -SH Chemistry of Life Chapter 23 Macromolecules Are large molecules composed of smaller molecules Are complex in their structures Macromolecules Most macromolecules are polymers, built from monomers Four classes of lifes organic molecules are polymers Carbohydrates

Proteins Nucleic acids Lipids A polymer Is a long molecule consisting of many similar building blocks called monomers Specific monomers make up each macromolecule (E.g. amino acids make proteins) The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration synthesis HO 1 2 3

H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO 1 2 H HO 3 H 2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer The Synthesis and Breakdown of Polymers

Polymers can disassemble by Hydrolysis (addition of water molecules) HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H (b) Hydrolysis of a polymer H

H 2O HO H Carbohydrates Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.) Sugars Monosaccharides Are the simplest sugars Can be used for fuel Can be converted into other organic molecules Can be combined into polymers Examples of monosaccharides Triose sugarsPentose sugars (C3H6O3) (C5H10O5) H O H Aldoses

C O Hexose sugars (C6H12O6) H C H O C H C OH H C OH H C OH


Glyceraldehyde H Ribose H C OH H HO C H C OH HO C H H

C OH H C OH H C OH H C OH H H Glucose H H C

Ketoses H C OH H C O Galactose H C OH H C OH C O O C OH H C OH

HO H H C OH H C OH Dihydroxyacetone H C OH H C OH H H C OH H Ribulose O

C C H H Fructose Monosaccharides May be linear Can form rings O H 1C H 2 HO 3 H H H C C

4 C 5 C 6 C 6 OH H OH OH OH CH2OH 5C H 4 C OH 3

H H O 5 H H OH C 6 1 H 2 C OH C H C OH C

H OH 4 O CH2OH 3 C H CH2OH O H 1 H 2 C OH 6 H C

OH 4 HO O 5 H OH 3 H H 1 2 OH OH H (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. Disaccharides

Consist of two monosaccharides Are joined by a glycosidic linkage (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units H forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the HO number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. H CH2OH CH2OH O H OH H H

H H OH HO H OH (b)Dehydration reaction in the synthesis of H sucrose. Sucrose is O O a disaccharide formed H H from glucose and fructose. Notice that fructose, though a hexose like Glucose glucose, forms a five-sided ring. O H H OHOH

H HO H O H H OH H2O O H CH2OH H 1 4 1 glycosidic linkage CH2OH H O H HO HO OH

H H H H CH2OH H HO H O H O H OH H 12 glycosidic 1 linkage H

O OH OH CH2OH O 2 H HO OH H H2O Fructose O H O H Maltose H H

4 OH CH2OH O H O Glucose Glucose CH2O H O H O H H H OH CH2OH Sucrose H CH2OH

Polysaccharides Polysaccharides Are polymers of sugars Serve many roles in organisms Storage Polysaccharides Chloroplas t Starch Starch Is a polymer consisting entirely of glucose monomers Is the major storage form of glucose in plants 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide

Glycogen Consists of glucose monomers Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m Glycogen (b) Glycogen: an animal polysaccharide Structural Polysaccharides Cellulose Is a polymer of glucose Has different glycosidic linkages than starch H H 4 H O

CH2O H O H OH H H O H O CH2O H O H O H H C H O H glucose H H O H

C H C H C O H H C C OH O H O H H 4 H O H

O H 1 H OH glucose (a) and glucose ring structures H O CH2O H O O H 1 4 O CH2O H O O H

1 O 4 CH2O H O O H CH2O H O 1 O 4 OH O O O O H H H H

(b) Starch: 1 4 linkage of glucose monomers CH2O O CH2O O H H H H O O O O O O O O H 1 4 H H O H H O O O CH2O CH2O O OH H

H H (c) Cellulose: 1 4 linkage of glucose monomers 1 O O H Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells

Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH CH2OH OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH O


Cellulose molecules A cellulose molecule is an unbranched glucose polymer. Cellulose is difficult to digest Cows have microbes in their stomachs to facilitate this process Figure 5.9 Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods Can be used as surgical thread CH2O HO OH H H OH H OH H H NH

C O CH3 (b) Chitin forms the exoskeleton (c) Chitin is used to make a (a) The structure of the of arthropods. This cicada strong and flexible surgical chitin monomer. is molting, shedding its old thread that decomposes after exoskeleton and emerging the wound or incision heals. in adult form. Lipids Lipids are a diverse group of hydrophobic molecules Lipids Are the one class of large biological molecules that do not consist of polymers Share the common trait of being hydrophobic Fats

Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Vary in the length and number and locations of double bonds they contain Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Fats Vary in the length and number and locations of double bonds they contain Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds Stearic acid (a) Saturated fat and fatty acid Unsaturated fatty acids

Have one or more double bonds Oleic acid (b) Unsaturated fat and fatty acid cis double bond causes bending Phospholipids Have only two fatty acids Have a phosphate group instead of a third fatty acid CH2 CH2 O O P O + N(CH ) 3 3 Choline Phosphate

O CH2 CH O O C O C CH2 Glycerol O Hydrophobic tails Hydrophilic head Phospholipid structure Consists of a hydrophilic head and hydrophobic tails (a) Structural formula Fatty acids Hydrophilic head

Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol The structure of phospholipids Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail Steroids Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings One steroid, cholesterol Is found in cell membranes Is a precursor for some hormones

H 3C CH3 CH3 HO CH3 CH3 Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes Proteins are made of monomers called amino acids An overview of protein functions Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the

Substrate reactant on which the enzyme acts. (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. Polypeptides Polypeptides Are polymers (chains) of amino acids A protein

Consists of one or more polypeptides Amino acids Are organic molecules possessing both carboxyl and amino groups Differ in their properties due to differing side chains, called R groups Twenty Amino Acids 20 different amino acids make up proteins CH3 CH3 H H3N+ C CH3 O H3N+ C H

Glycine (Gly) O C H3N C + O C H H3N C H Valine (Val) Alanine (Ala) CH2 O

CH2 CH CH3 CH3 O CH3 CH3 C + O O C H3C H3N + O CH

C O C H Leucine (Leu) H Isoleucine (Ile) O Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H CH2

O H3N+ C O Methionine (Met) C H CH2 O H3N+ C O Phenylalanine (Phe) C H O H2C CH2 H2N

C O C H C O Tryptophan (Trp) Proline (Pro) O OH OH Polar CH2 H3N C + CH

O H3N C + O H Serine (Ser) C O C H3N + O H CH2 C CH2

O C H Threonine (Thr) H3N O C + CH2 O C H3N H O Electrically charged H3N +

O O NH3+ NH2 C CH2 C CH2 CH2 CH2 CH2 CH2 CH2 CH2 O C H

H3N + C O CH2 C H O H3N + C O + C O C O H

Glutamic acid (Glu) NH2+ O H3N + C H NH CH2 H3N + C H CH2 C Lysine (Lys) NH+ CH2

O H Aspartic acid (Asp) C CH2 Asparagine Glutamine (Gln) (Asn) C O H3N Basic O C CH2 O H

Tyrosine (Tyr) Cysteine (Cys) C + O Acidic C NH2 O C SH CH3 OH NH2 O O C

O O C O Arginine (Arg) Histidine (His) Amino Acid Polymers Amino acids Are linked by peptide bonds Protein Conformation and Function A proteins specific conformation (shape) determines how it functions Four Levels of Protein Structure Primary structure H3N Amino end Is the unique sequence of amino

acids in a polypeptide Amino acid subunits GlyProThrGly Thr Gly + Glu CysLysSeu LeuPro Met Val Lys Val Leu Asp AlaVal ArgGly Ser Pro Ala GluLle Asp Thr

Lys Ser Lys Trp Tyr LeuAla Gly lle Ser ProPheHis GluHis Ala Glu Val AlaThrPheVal Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Tyr ThrSer Leu Ser

Pro SerTyr Thr Ala Val Val Glu ThrAsnProLys Figure 5.20 c o o Carboxyl end Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the helix and the pleated sheet pleated sheet O H H C C N

Amino acid subunits C N H R R C C N O H H H O H H C C N C C N OH H R O C H R


helix R O H H C C N C C N OH H R O C H H H C N HC C N HC N C N H H C O C C O R R O N


N HC N H O C Tertiary structure Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups CH2 CH 2 O Hyrdogen H O bond H 3C CH CH3 H 3C CH3 CH HO C CH2 Hydrophobic interactions and

van der Waals interactions Polypeptid e backbone CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptid e chain Collage n Chains Iron Heme Chains Hemoglobin

Review of Protein Structure H3N Amino end + Amino acid subunits helix What Determines Protein Conformation? Protein conformation Depends on the physical and chemical conditions of the proteins environment Temperature, pH, etc. affect protein structure Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Denatured protein Normal protein Renaturation Nucleic Acids

Nucleic acids store and transmit hereditary information Genes Are the units of inheritance Program the amino acid sequence of polypeptides Are made of nucleotide sequences on DNA The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) Deoxyribonucleic Acid DNA Stores information for the synthesis of specific proteins Found in the nucleus of cells DNA Functions Directs RNA synthesis (transcription) Directs protein synthesis through RNA DNA (translation) 1 Synthesis of mRNA in the nucleus

NUCLEUS 2Movement of mRNA into cytoplasm via nuclear pore mRNA CYTOPLASM mRNA Ribosome 3 Synthesis of protein Polypeptide Amino acids The Structure of Nucleic Acids 5 end Nucleic acids Exist as polymers called polynucleotides 5C

O 3C O O 5C O 3C (a) Polynucleotide, or nucleic acid OH 3 end Each polynucleotide Consists of monomers called nucleotides Sugar + phosphate + nitrogen base Nucleoside Nitrogenous base O

O P 5C O CH2 O O Phosphate group (b) Nucleotide 3C Pentose sugar Nucleotide Monomers Nucleotide monomers Are made up of nucleosides (sugar + base) and phosphate groups

Nitrogenous bases Pyrimidines NH2 O O C CH C C 3 N CH C CH HN HN CH C CH C C CH N N O N O O H H H CytosineThymine (in DNA)

Uracil (in RNA) RNA) Uracil (in U C U T Purines NH2 O C N N C C NH N HC HC C CH N C N NH2 N N H H Adenine Guanine A

G C 5 Pentose sugars HOCH2 O OH 4 H H 1 5 HOCH2 O OH 4 H H 1 H H H 3 2 H 3 2 H OH OH OH Deoxyribose (in DNA)

Ribose (in RNA) (c) Nucleoside components Nucleotide Polymers Nucleotide polymers Are made up of nucleotides linked by theOH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next Gene The sequence of bases along a nucleotide polymer Is unique for each gene The DNA Double Helix Cellular DNA molecules Have two polynucleotides that spiral around an imaginary axis Form a double helix The DNA double helix Consists of two antiparallel nucleotide strands 5 end

3 end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands A 3 end Nucleotide about to be added to a new strand 5 end 3 end 5 end New strands 3 end A,T,C,G The nitrogenous bases in DNA

Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) DNA and Proteins as Tape Measures of Evolution Molecular comparisons Help biologists sort out the evolutionary connections among species

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