AP Biology Organic Chemistry

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organic chemistry
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the study of carbon compounds. Most carbon compounds contain hydrogen compounds.
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Carbon
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most versatile element because of its 4 open bonds, naming it “tetravalent.” All organic molecules have carbon in them. Very abundant in the world.
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vitalism
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the belief in a life force outside the jurisdiction of physical and chemical laws. This idea was falsified because scientists can create organic compounds with inorganic substances.
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mechanism
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the view that physical and chemical laws govern all natural phenomena including the processes of life.
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Majority of the organic molecules are composed of:
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Oxygen, Hydrogen, Nitrogen, Carbon, Potassium,
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Different ways Carbon can differ
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– chain (length of chain) – branching – Double bond position – Presence of rings
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Hydrocarbons
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organic molecules consisting of only carbon and hydrogen
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fats
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long chains of hydrocarbons attached
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Combustion of hydrocarbons produce…
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A TON OF ENERGY!!!
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Isomers
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compounds with the same atoms and # of atoms, just arranged differently with different properties.
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To uphold a fashion sense, true biologists…
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wear designer GENES. LOL. If you didn’t think that was funny, get a life.
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Structural isomers
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differ in covalent arrangement of their atoms.
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CIS- Trans Isomers
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different arrangement around a double bond
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Enantiomer
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Mirror images of the molecule/compound. Generally one is active, while other one is inactive.
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What do you know about: Hydroxyl
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(-OH) Bonded with a carbon skeleton, don’t mix with hydroxide ion, Polar. Example: Alcohol.
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What do you know about: Carboxyl
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(-COOH) Is in amino acids, If dissolved in water, you guessed it. it’s acidic. Example: Carboxylic Acid.
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What do you know about: Carbonyl
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(=CO) Example: Keytones, Aldehydes. Found in sugar. Example: Glucose.
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Amino
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(-NH2) Amines. In amino acids. Act basic because can pick up a H+ from surroundings in water. Example: Glycine
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Sulfhydryl
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(-SH) Cross-link of two sulfhydryl structures bring more stability to proteins.
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Phosphate
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(PO4) contain 2- charge, can react with water creating energy. Many examples: Phospholipid
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Methyl
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(-CH3) Addition of a methyl group to DNA. Interesting fact: Arrangement of methyl groups determines male or female sex hormone. Example: Methyl Alcohol.
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ATP
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Adenosine Tri-Phosphate. Primary energy source for the body of any organism.
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macromolecules
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carbohydrates, lipids, proteins, and nucleic acids are large molecules. (Ex: Protein = 100,000 daltons)
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polymer
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A long molecule consisting of many similar or identical liked by covalent bonds
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Monomer
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individual units in a polymer
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enzymes
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specialized macromolecules designed to speed up chemical reactions
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dehydration synthesis reaction
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putting substances together by removing water from the substances
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hydrolysis
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breaking up covalent bonds by adding water (general note: “lysis” means to break up.
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Carbohydrates (generally end with -ose)
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sugars and polymers of sugars
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monosaccharide
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single sugar molecule (example: glucose)
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disaccharide
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double sugar chain (example: sucrose)
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glycosidic linkage
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covalent bonds between monosaccarides after dehydration synthesis.
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polysaccharides
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long chains of sugar macromolecules.
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starch
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a polymer of glucose monomers, as granules within cellular structures known as plastids which include chloroplasts.
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Stockpile glucose
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a storage of glucose that is hydrolyzed to get energy
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Glycogen
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branched polymer for glucose storage in liver for an animal.
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cellulose
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structural polymer of glucose. Is used to make up the cell wall of plant cells. Note, the human body cannot break up cellulose because it doesn’t have the enzyme to do so: Cellulase. However, it is used as fiber n the body.
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Chitin (pronounced KITE-in)
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another structural polysaccharide is used by arthropods to build their exoskeleton. Doctors use a thread of chitin to stitch up patients from surgeries.
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lipids
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mix poorly if at all with water. Mostly hydrocarbons. – Fats – Phospholipids – steroids
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fatty acid
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long carbon skeleton, with a carboxyl group on it at the end.
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Fat
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a glycerol molecule with 3 fatty acid chains. This is also called “triglyceride.” Primary goal is to STORE energy
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saturated fats
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all hydrogen bondin sites are taken. No double bonds. At room temperature, are solids. Example: Butter.
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Unsaturated fats
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has one or more double bonds. Liquid at room temperature. Has a CIS bond.
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Hydrogenated
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unsaturated fat converted to saturated by adding hydrogens and opening up bonds.
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Trans-fat
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has “TRANS” bonds instead of CIS bonds.
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Phospholipids
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make up cell membrane, and example of how form fits function. Has a Choline, Phosphate, Glycerol, and two fatty acid chains. This makes the “head” hydrophilic (attracted to water) and the tail hydrophobic (repellent from water)
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hydrophilic
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attracted to water
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hydrophobic
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repellent from water
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steroids
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carbon skeleton with 4 fused rings
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cholesterol
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common component on cell membrane, and is a precursor to to other steroids. Synthesized in the liver.
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PROTEINS
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are important, and account for 50 percent of dry mass of cells. Biologically functional molecule that consists of one or more polypeptides each folded and coiled into a specific 3D structure.
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catalysts
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chemical a gens that selectively speed up chemical reactions without being consumed in the reaction
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polypeptides
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polymers of amino acids
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Amino acids
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an organic molecule possessing both amino groups and carboxyl groups
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Functions of Proteins
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– Enzymes – Defense structure – Storage – Transport – Hormonal proteins – receptor protein – contractile and motor protein – structural protein.
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How many Amino Acids are there?
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20 amino acids. Learn them. make real note cards.
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Peptide bonds
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covalent bond between amino acids. Many of these generate chains called polypeptides. A form of Dehydration synthesis.
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Fredrick Sanger
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determined the peptide sequence
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Globular proteins
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sorta spherical in shape. Think “glob”
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Fibrous proteins
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long fiber proteins.
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Primary structure of proteins
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individual amino acids linked to other animo acids. Backbone of the chain.
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Secondary structure of proteins
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peptide strand existing with other polypeptide strands with hydrogen bonds in the form of alpha-helix (more common, stronger in structure, think DNA formation) and beta-sheets (less common, think opened folded paper)
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Tertiary structure
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secondar structures join and interact between each other. Have helixes and sheets in them interacting through ALL DIFFERENT BONDS. Many proteins stop here.
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hydrophobic interactions
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once the polypeptide is in its functional shape, the non polar side chains end up in the middle.
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Quaternary Structures
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overall protein structure that results from the aggregation of the polypeptide sub units.
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Mutations and how “Structure fits function” principle
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1 Mutation can cause a huge change, because it changes the interaction of the protein with it’s environment. Example: Sickled blood cell v. Normal blood cell. (KNOW THIS EXAMPLE!)
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Sickle-cell disease
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blood disorder cause db an amino acid switching with another similar amino acid. This causes changes in the function of the polypeptide.
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Denaturation
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protein loses its functional shape and unravels due to changes in environment that weaken the weak bonds within the polypeptide. (Caused by heat and pH fluctuations)
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Renaturation
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protein goes back to normal when proper conditions are resorted. It will return back to normal function.
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Chaperonins
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protein molecules that assist in the proper folding of other proteins. They don’t themselves determine shape, but protect the polypeptide.
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X-Ray Crystallography
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determine the 3D structure of molecules
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Gene
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A chain of amino acids that is passed through a method of desecrate inheritance consisting of DNA
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Nucleic Acid
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polymers of monomers called nucleotides
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DNA
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deoxyribonucleic acid. Holds the amino acids in a double helix. Provides the instruction for their own replication.
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RNA
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Ribonucleic Acid. Think of one side of a DNA strand.
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Production of Protein
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DNA > mRNA > Protein
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Nucleic Acid structure
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Phosphate group, pentose sugar, and nitrogenous base, which determines what nucleotide it is.
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polynucleotides
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polymers of nucleic acids
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nucleotides
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monomers of a polynucleotide
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nucleoside
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side of the cyclic acid without any phosphate
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pyrimidine
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Cytosine and Thymine nucleotides. Bond with Purines.
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Purines
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Adenine and Guanine. Bond with Pyrimidines.

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