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Mr. Dill AP Biology

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Organic molecules are any molecules that contain atoms from three elements: carbon, hydrogen, and oxygen. For example, glucose is organic, since its molecular formula is C 6 H 12 O 6 Carbon dioxide (CO 2 ) is inorganic since it does not contain hydrogen. Covalent bonds link carbon atoms together in long chains that form the skeletal framework for organic molecules. These carbon skeletons may vary in: Length Shape (straight chain, branched, ring) Number and location of double bonds Other elements covalently bonded to available sites

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All organic molecules have two parts: The carbon backbone & the functional group Tetravalence of carbon allows for complex arrangement of carbon compounds Carbon atoms can form single, double, or triple covalent bonds

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(a) Methane (b) Ethane (c) Ethene (ethylene) Molecular Formula Structural Formula Ball-and- Stick Model Space- Filling Model H H H H H H H H H H HH H H C C C CC CH 4 C2H6C2H6 C2H4C2H4 Name and Comments Hydrocarbons Are molecules consisting of only carbon and hydrogen Hydrocarbon chains are hydrophobic because the CC and CH bonds are nonpolar

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(a) A fat molecule (b) Mammalian adipose cells 100 m Fat droplets (stained red) Figure 4.6 A, B Found in fossil fuels and makes up the tails of lipids

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groups of atoms acting as a unit, that give organic molecules their physical properties,their chemical reactivity, & solubility in aqueous solutions. most possess electronegative atoms (N, P, O, S... EASILY ATTRACT PROTONS) key bonds are : ester (C-O-C) & amide (O=C-N-) are ionizable at physiological pH -NH 2 AMINE= amino acid -C=O x CARBONYL= aldehyde/ketone -COOH x CARBOXYL= acid -OH x HYDROXYL = alcohol -PO 4 PHOSPHORYL= organic phosphate -SH SULFHYDRYL= disulfide -CH 3 METHYL= hydrocarbon

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Polar group; the bond between the oxygen and hydrogen is a polar covalent bond. Makes the molecule to which it is attached water soluble. Polar water molecules are attracted to the polar hydroxyl group which can form hydrogen bonds. Organic compounds with hydroxyl groups are called alcohols.

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Functional group that consists of a carbon atom double-bonded to oxygen (-C=O) Is a polar group. The oxygen can be involved in hydrogen bonding, and molecules with his functional group are water soluble. Is a functional group found in sugars. Aldehyde = carbonyl group on end carbon of chain Ketone =- carbonyl group attached to internal carbon

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Functional group that consists of a carbon atom which is both double- bonded to an oxygen and single-bonded to the oxygen of a hydroxyl group (-COOH). Is a polar group and water soluble. The covalent bond between oxygen and hydrogen is so polar, that the hydrogen reversibly dissociates as H +. This polarity results from the combined effect of the two electronegative oxygen atoms bonded to the same carbon. Since it donates protons, this group has acidic properties. Compounds with this functional group are called carboxylic acids. Carboxyl Group

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Functional group that consists of a nitrogen atom bonded to two hydrogen atoms & to the carbon skeleton (NH 2 ). Is a polar group and soluble in water. Acts as a weak base. The unshared pair of electrons on the nitrogen can accept a proton, giving the amino group a +1 charge. Organic compounds with this function group are called amines.

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Functional group which consists of an atom of sulfur bonded to an atom of hydrogen (SH). Stabilize the structure of proteins. (Disulfide bridges of proteins) Organic compounds with this functional group are called thiols.

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Functional group which is the dissociated form of phosphoric acid (H 3 PO 4 ). Loss of two protons by dissociation leaves the phosphate group with a negative charge. Has acid properties since it loses protons. Polar group and soluble in water. Organic phosphates are important in cellular energy storage and transfer

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methyl group (CH 3 ) Non-polar hydrophobic functional group

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Organic compounds are formed by polymerization Large carbon compounds are built up from smaller simpler molecules called MONOMERS Monomers can bind to one another to form complex molecules known as POLYMERS Macromolecules are very large polymers

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Monomers link to form polymers through a chemical reaction called a CONDENSATION REACTION or Dehydration Synthesis Water is released during the formation of polymers The BREAKDOWN of some complex molecules, such as polymers, occurs through a process known as HYDROLYSIS Hydrolysis is the reversal of a condensation reaction

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Dehydration Synthesis

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Hydrolysis

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Carbohydrates (C-H-O 1:2:1 ratio) Lipids (C-H-O) Proteins (C-H-O-N)sometimes S Nucleic Acids (C-H-O-N-P)

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MONOSACCHARIDES are simple sugars in a 1:2:1 ratio GLUCOSE GALACTOSE = sugar found in milk FRUCTOSE = fruit sugar Chemical composition (C 6 H 12 O 6 )

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Glucose

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glycosidic linkage DISACCHARIDES consist of two single sugars(monosaccharides) linked together by glycosidic linkage (Dehydration synthesis) Lactose = Milk sugar Sucrose = Table sugar

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POLYSACCHARIDE is a carbohydrate made of long chains of sugars (3 or more monosaccharides) Starch - Plants convert excess sugars into starches for long- term storage (Alpha linkage) Glycogen -Animals store glucose in the form of polysaccharide glycogen in the liver and muscles to be used as quick energy Cellulose -a structural polysaccharide contained in the cell walls of plants ( linkage) Chitin a polysaccharide found in the cell walls of fungi and the exoskeletons of insects and arthropods

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Glucose

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Lipids are large, NONPOLAR organic molecules that DO NOT dissolve in water Oils, fats, waxes, and steroids are lipid based Lipid molecules use less OXYGEN than carbohydrates to store energy efficiently Used in biological membranes and as chemical messengers Monomers Fatty acids & Glycerol

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UNSATURATED FATS are a liquid at room temperature (OILS). Double bonds can have hydrogen added SATURATED FATS are solid at room temperature NO double bonds

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Stearic acid Solid at room temp Oleic acid Liquid at room temp

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Hydrophilic = Water loving Hydrophobic = Water fearing

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Chemical composition C-H-O-N-S Proteins are made up of smaller monomers called AMINO ACIDS Amino Acids differ ONLY in the type of R group they carry Amino acids composed of 3 parts 1. Amino Group 2. Carboxylic group 3. R-group (Makes 20 different amino acids)

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Each protein has a specific, and complex shape Different shapes allow proteins to perform different functions Two Amino Acids bond to form a DIPEPTIDE during a condensation reaction (2 Amino Acids form a covalent bond, called a PEPTIDE BOND) Amino Acids can bond to each other one at a time, forming a long chain called a POLYPEPTIDE. Proteins are composed of one or more polypeptides.

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Primary Structure sequence of amino acids Secondary structure Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid. R groups are NOT involved. Tertiary structure disulfide bridges, ionic bonding, or h-bonding of R-groups Quaternary structure 2+ amino acid chains R- group interactions, H bonds, ionic interactions

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Amino acid structure: NH 3 - C - COOH Amino acids differ due to the R group The structure of the R-group determines the chemical properties of the amino acid

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The polar uncharged amino acids are hydrophilic & can form h-bonds Serine Threonine Glutamine Asparagine Tyrosine Cysteine

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The nonpolar amino acids are hydrophobic and are usually found in the center of the protein. They also found in proteins which are associated with cell membranes. Glycine Alanine Valine Leucine Isoleucine Methionine Phenylalanine Tryptophan Proline)

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The electrically charged amino acids have electrical properties that can change depending on the pH. Aspartic Acid Glutamic Acid Lysine Arginine Histidine

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The electrically charged amino acids (Aspartic Acid, Glutamic Acid, Lysine, Arginine, and Histidine) have electrical properties that can change depending on the pH. Cysteine can form covalent disulfide bonds Proline had a unique structure and causes kinks in the protein chain When two amino acids are joined together, the bond formed is called a peptide bond

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Transfer protein from aqueous solution to an organic solvent (chloroform) Any chemical that disrupts h-bonds, ionic bonds, & disulfide bridges Excessive heat Changes in pH

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Act as CATALYSTS that can speed up some reactions by more than a billion times! Enzymes work by a physical fit (Lock and Key) between the enzyme molecule and its SUBSTRATE, the reactant being catalyzed. Enzymes reduces the activation energy for the chemical reaction to occur. After the reaction, the enzyme is released and is unchanged, so it can be used many times Enzyme names end in -ase

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Enzyme & Substrate fit like a lock & key (Shape specific) pH or temperature can change the active site shape on any enzyme Active site is where the reactants bind to the enzyme

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The energy require to start a reaction is called Activation Energy

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RNA and DNA made of nucleic acids C-H-O-N-P atoms Polymers of nucleotides Nucleotides consist of a 5-carbon sugar, a phosphate group, and a nitrogenous base. Store and transmit genetic information

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Nucleic Acids

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