Presentation on theme: "Organic Chemistry Organic chemistry is the study of carbon-based molecules. Nearly all of the compounds that a cell makes are composed of carbon bonded."— Presentation transcript:
2 Organic ChemistryCarbon is unparalleled in its ability to form large, diverse molecules.Recall that carbon has six electrons:2 in its innermost shell and 4 in its outermost shellCCarbon completes its outer shell by sharing electrons with other atoms in 4 covalent bonds.
4 Organic ChemistryCarbon can share its electrons with four hydrogen atoms, creating CH4 or methane.CHMethane is an example of an organic compound and is the simplest of all organic compounds.
5 Organic CompundsWhen Carbon shares electrons with Hydrogen atoms, a hydrocarbon resultsHydrocarbons are the major components of petroleumPetroleum (crude oil) consists of the partially decomposed remains or organisms that lived millions of years agoThis is why the burning of fossil fuels increases carbon dioxide into our atmosphereCH4 + 2 O2 → 2 H2O + CO2 + Energy
6 Organic ChemistryThe unique properties of an organic compound depend upon the size and shape of its carbon skeleton and the groups of atoms that are attached to that skeleton. Of the six groups of atoms that are essential to life, five serve as functional groups. Functional groups affect a molecule’s function by participating in chemical reactions in characteristic and predictable ways.carbon skeleton: the chain of carbon atoms in an organic molecule
7 Hydroxyl group – polar, consists of a Hydrogen bonded to an Oxygen Carbonyl group – polar, Carbon linked by a double bond to an OxygenCarboxyl group – polar, a Carbon double-bonded to both an Oxygen and a Hydroxyl groupAmino group – polar, composed of a Nitrogen bonded to 2 Hydrogen atoms and the Carbon skeletonPhosphate group – polar, consists of a Phosphorus atom bonded to 4 Oxygen atomsMethyl group – nonpolar and not reactive,Carbon bonded to 3 Hydrogen
8 Same structure, but different functional groups Estradiol – female sex hormoneMethyl groupFemale LionHydroxyl groupCarbonyl groupTestosterone – male sex hormoneMale Lion
9 Besides water, all biological molecules are organic, or carbon-based Besides water, all biological molecules are organic, or carbon-based. There are many organic molecules, but most of the human body is made up of just four types: carbohydrates, lipids, proteins and nucleic acids.
10 Carbohydrates, lipids, proteins and nucleic acids are called macromolecules, and are the building blocks of cells and their chemical machinery. Cells make most of these large molecules by joining together smaller molecules, or monomers, into chains called polymers.Cellular structurePolymerMonomerChromosomeDNA strandNucleotideNucleic Acid
11 The key to the great diversity of macromolecules is in the arrangement of its monomers. DNA is built up of only four monomers (nucleotides), and proteins are made with only twenty monomers (amino acids), but both macromolecules are incredible diverse. The proteins in you and a fungus are made with the same twenty amino acids!
12 A cell links monomers together to form polymers by way of a dehydration reaction. A dehydration reaction is so named because it results in the removal of a water molecule. An unlinked monomer has a hydroxyl group (--OH) at one end, and a hydrogen atom (--H) at the other end.Hydrogen atomHydroxyl group
13 Dehydration ReactionpolymermonomerHydrogen atomHydroxyl groupBy removing the hydroxyl group of the polymer, and the hydrogen atom of the monomer that is being added, a water molecule is released.
15 Just as removing a water molecule links monomers together (to form polymers), the addition of a water molecule breaks a polymer chain apart (releasing a monomer). The process of breaking up polymers is called hydrolysis. Hydrolysis is essentially the reverse of a dehydration reaction. Hydrolysis is necessary to break down polymers that are too large to enter a cell otherwise.
18 EnzymesBoth dehydration reactions and hydrolysis require the help of enzymes to make and break bondsEnzymes are specialized proteins that speed up the chemical reactions in cellsEnzymes are extremely important – without them, many reactions cannot take place. If you lack lactase, you cannot hydrolyze the bond in lactose
19 Carbohydrates are polymers made up of carbon, hydrogen, and oxygen atoms. Carbohydrates play important roles in the energy storage and structural support of organisms, and are themselves an excellent source of energy.Carbohydrcarbonhydrogenoxygen
23 Monosaccharides can also be linked together to form polysaccharides. A polysaccharide is a large polymer consisting of hundreds or thousands of monosaccharides linked by dehydration reactions.Polysaccharides function as storage molecules or structural compounds.The most common types of polysaccharides are starch, glycogen, cellulose, and chitin.
25 Through the process of photosynthesis, plants produce glucose as an energy source. Often, a plant produces more glucose than is readily needed, so the plant stores this energy as long chains of glucose molecules, or starch! Starch is found in potatoes and grains, such as wheat, corn and barley.
26 Polysaccharide: Glycogen Glycogen is an energy storage polysaccharide used by animals. Glycogen also consists entirely of repeating glucose monomers, but is much longer and more branched than starch. Glycogen is broken down into glucose as energy is needed.
27 Polysaccharide: Cellulose Cellulose is a structural polysaccharide used by plants. Cellulose is the most abundant organic compound on Earth, forming the cell walls of all plant cells.
28 Polysaccharide: Cellulose Cellulose consists of long chains of glucose molecules linked in such a way that they can not be broken down easily. Humans are unable to digest cellulose and it makes up the fiber in our diets. Certain microbes can digest cellulose, and reside in the guts of herbivores, such as cows, sheep, and even termites!
30 Polysaccharide: Chitin Chitin is a structural polysaccharide used by animals. Animals that use chitin for external skeletons include insects and crustaceans. Fungi also have chitin in their cell walls for structural support. Chitin attaches to proteins forming a tough and resistant protective material.
36 Lipids: FatsA fatty acid consists of a long chain of carbon and hydrogen atoms.The arrangement of these atoms can vary, affecting the fat molecule’s physical properties.Fats whose fatty acids contain the maximum number of hydrogen atoms that can fit are called saturated fats.
40 Who You Calling Fat?! Triglycerides (fats and oils): Store energy Insulate (blubber, etc)Provide cushioningPrevent dehydrationHelp to maintain internal temperature
41 Lipids: Phospholipids Phospholipids are structurally similar to fats, but contain only 2 fatty acids attached to a glycerol molecule.Each phospholipid molecule has a polar, or hydrophilic end, and a non-polar, or hydrophobic end.Phospholipids are the main component of cellular membranes.
43 Lipids: Phospholipids The membranes of all cells are composed of two layers of phospholipids, called a bi-layer.The polar, hydrophilic ‘heads’ face outward and are in contact with the aqueous environment on either side of the membrane.The non-polar, hydrophobic ‘tails’ cluster together in the middle of the membrane.
46 Lipids: SteroidsCholesterol is a common steroid found in animal cell membranes.Cholesterol is also part of some sex hormones like testosterone, estrogen and progesterone.CholesterolTestosteroneEstrogen
54 Secondary StructureThe many hydrogen bonds within the polypeptide chain of silk fibers make spider fiber as strong as steel; uses of silk proteins include fishing line, surgical thread and bulletproof vests!
56 Quaternary StructureThe quaternary structure of a protein describes the complex association of multiple polypeptide chains.Not all proteins consist of 2 or more polypeptide chains, but those that do have a quaternary structure.Each polypeptide chain in the association has its own primary, secondary, and tertiary structures.
58 Quarternary Structure PolypeptidechainCollagen is formed by several polypeptide chains in a rope-like arrangementGives connective tissue, bone, tendons, and ligaments its strength!Hemoglobin is another example of a quarternary structure protein (transports oxygen in blood)Collagen
61 Proteins gone bad So what happens is a protein folds incorrectly? Many diseases, such as Alzheimer’s and Parkinson’s involve an accumulation of misfolded proteinsPrions are infectious agents composed of proteinsPrion diseases are currently untreatable and always fatal
62 PrionsPrions infect and propogate by refolding abnormally into a structure that is able to convert normally-folded molecules into abnormally-structured formThis altered form accumulates in infected tissue, causing tissue damage and cell deathPrions are resistant to denaturation due to their extremely stable, tightly packed structure
63 PrionsPrions are implicated in a number of diseases in a variety of mammals:Bovine Spongiform Encephalopathy (“Mad Cows Disease”) – spread by feed containing ground-up infected cattleCreutzfeldt-Jakob Disease – degenerative neurological disorder spread by skin grafts or human growth hormone products; Kuru is a similar disease spread by cannibalism among the Fore tribe of Papua New Guinea
64 PrionsChronic Wasting Disease – found in deer, moose, elk in U.S. and CanadaFatal Familial Insomnia – very rare, inherited prion disease (50 families worldwide have the responsible gene mutation); insoluble protein causes plaques to develop in the thalamus, the region of brain responsible for the regulation of sleep; fatal within several months
65 Proteins gone bad (or maybe not…) Sickle cell anemia is caused by a genetic mutation of hemoglobin (not a prion); causes a sickling of the red blood cellThose with 2 copies of the mutated gene have a reduced life expectancy; those with only 1 copy have “Sickle trait” – cells only sickle under reduced oxygen loadSickle cell disease common in tropical and subtropical regions where malaria is common; provides a selective advantage against malaria!
66 Sickle Cell Anemia Remember natural selection is a pessimistic process Sickle blood cellsRemember natural selection is a pessimistic processThose with the sickle cell mutation survive malaria infestation better than those without“Heterozygous advantage”Normal red blood cell
80 The Double HelixDNA’s double helix results from hydrogen bonds formed between its nitrogenous bases.Large nitrogenous bases (adenine and guanine) pair with smaller bases (thymine and cytosine).Adenine bonds with thymine (A-T) and guanine bonds with cytosine (G-C).
83 DNA double helixThe 2 DNA chains are held in a double helix by hydrogen bonds between their paired basesMost DNA molecules have thousands or millions of base pairs(A and T would be considered a base pair; as would C and G)