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Transcript
Bonding, to get the octet ◦ The interactions that make bonds are called chemical reactions and have reactants (left side of the arrow) and products (right side of the arrow) Molecule= simplest part of a compound ◦ Chemical formula: ex: CH4 Ionic bonds=Ions are formed due to sharing of electrons. ATTRACTION! Covalent bonds= Sharing electrons ◦ Involve only 1 type of atom b/c have the same electron affinity Polar-covalent bonds= Sharing electrons ◦ Involve different types of atoms b/c have different electronegativities (attraction of an atom for e- of a covalent bond) Necessary for most chemical signaling between cells ◦ Ionic Bond ◦ Hydrogen bond=Occurs when H is covalently bonded to N or O (usually) and is attracted to the electronegative part of another molecule ◦ Van der Waals interactions=as electrons move, even in non-polar molecules, attraction points occur because of temporary polarity EX: Gecko walking up walls + – Water (H2O) + Hydrogen bond – Ammonia (NH3) + + + Water is a polar molecule ◦ Overall charge is unevenly distributed Water’s “bent” geometry allows for hydrogen bonding-Note: this is NOT just a covalent bond! It’s a special case of an interaction in which the partial + H is attracted to the electrons orbiting the O on the other water molecule (just as Na+ is attracted to Cl-) This tends to make water “sticky,” giving it unique properties Hydrogen bond + + Polar covalent bonds + + Cohesion and Adhesion-Water is attracted to itself (cohesion) and to other polar substances (adhesion) Contributes to movement of water & dissolved nutrients against gravity in plants Water is a very versatile biologic solventmolecules surround substances and separate them Water expands when it freezes because of the tetrahedral arrangement of its molecules Becomes less dense & expands b/c of hydrogen bonding Ice is fully hydrogen-bonded while liquid water only contains temporary hydrogen bonds Adhesion Two types of water-conducting cells Cohesion Direction of water movement 300 m Hydrogen bond Ice: Hydrogen bonds are stable Liquid water: Hydrogen bonds break and re-form Heat=kinetic energy of the molecules in a substance (temperature is a measure of this energy) Like all energy, the flow of heat goes from high(warm) to low(cool) ◦ Ice absorbs the heat from water to cool your drink-it does NOT release “cold” “Cold” does not exist in a thermodynamic sense! It’s simply the removal (absorption) of heat (kinetic energy) Biochemistry Valence=? Capable of single bonds (-ane), double bonds (-ene), and triple bonds (-yne) Readily forms hydrocarbons (organic molecules of only C & H), which are the backbones of biochemicals Carbon molecules often form isomers (same formula, different architecture) ◦ Isomers can be Structural (chains vs. rings), cis-trans (variation around a double bond), or enantiomers (mirror images which vary around an asymmetric central carbon) ◦ Real world applications: vision affected by cis trans, trans fats, pharmaceuticals) (a) Structural isomers (b) Cis-trans isomers cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (c) Enantiomers CO2H CO2H H NH2 CH3 L isomer NH2 H CH3 D isomer Miller & Urey experiment ◦ Concluded complex molecules could arise spontaneously from conditions on early earth Amino acids, formaldehyde, hydrocarbons Functional groups are used to distinguish molecules made up of C, H, O, since these groups cause the molecules to behave differently: ◦ ◦ ◦ ◦ ◦ ◦ ◦ Hydroxyl group (OH-) Carbonyl group (C=O) Carboxyl group (COOH) Amino group (NH2 ) Sulfhydryl group (SH) Phosphate group (PO4) Methyl (CH3 ) ◦ Use the chart in your text to make key word flash cards! CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) NAME OF COMPOUND Alcohols (Their specific names usually end in -ol.) Ketones if the carbonyl group is within a carbon skeleton Carboxylic acids, or organic acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol Acetone Acetic acid Propanal FUNCTIONAL PROPERTIES • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. • A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). • Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar: Nonionized Ionized • Found in cells in the ionized form with a charge of 1 and called a carboxylate ion. Amino Sulfhydryl Phosphate Methyl (may be written HS—) Amines Organic phosphates Thiols Glycine Cysteine Glycerol phosphate • Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): • Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. • Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as above; 1– when located internally in a chain of phosphates). • Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. • Molecules containing phosphate groups have the potential to react with water, releasing energy. Nonionized Ionized • Found in cells in the ionized form with a charge of 1+. Methylated compounds 5-Methyl cytidine • Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. • Arrangement of methyl groups in male and female sex hormones affects their shape and function. Model Tasks 1&2 ◦ To be graded as part of your notes. ◦ 15 minutes Monomer=1 subunit (link in a chain) Polymer=a chain of small subunits Polymers are put together by dehydration synthesis reactions ◦ Monomers joined covalently losing a water molecule Polymers are taken apart by hydrolysis (hydro=water, lysis=splitting) ◦ Broken down into monomers, water must be broken to fulfill the valence of the open bonds. ◦ Digestion is an example of this happening in our bodies All Biochemicals are polymers (a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond. 1 2 3 4 Longer polymer (b) Hydrolysis: breaking down a polymer 1 2 3 Hydrolysis adds a water molecule, breaking a bond. 1 2 3 4 Model Task 3 ◦ To be graded as part of your notes. ◦ 15 minutes Energy Source! Sugars are mono- or disaccharides ◦ Ex: glucose(mono), sucrose (di) ◦ Disaccharides-joined by glycosidic linkage (covalent bond formed btwn 2 monosaccharides) Polysaccharides • Have hundreds to thousands of monomers. • Animals use glycogen for energy and chitin for structure. • Plants use cellulose for structure and use Starch: amylose or amylopectin for energy. • There are difference is in the types of glycosidic linkage between the monomers and the degree of branching within the molecules. Chloroplast Starch granules Amylopectin Amylose (a) Starch: 1 m a plant polysaccharide Mitochondria Glycogen granules Glycogen (b) Glycogen: 0.5 m an animal polysaccharide Cellulose microfibrils in a plant cell wall Cell wall Microfibril 10 m 0.5 m Cellulose molecules Glucose monomer The structure of the chitin monomer Chitin forms the exoskeleton of arthropods. Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Model Task 4 ◦ To be graded as part of your notes. ◦ 15 minutes Fats, oils, waxes Non-polar ◦ Exception: phospholipids (part hydrophilic, part hydrophobic) Energy storage, insulation, protective coverings (chemically stable, takes a lot to break them apart) 1 g fat stores more than 2x energy of polysaccharide Composed of Fatty Acid chains Glycerol This is an Ester Linkage 3 Fatty Acids Saturated Unsaturated Full of hydrogen atoms Few hydrogen atoms Single bonds Double and Triple bonds Ex. Butter Ex. Canola Oil Unhealthy Healthy (a) Saturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid (b) Unsaturated fat Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Cis double bond causes bending. What’s a trans-fat? ◦ Unsaturated fat that has trans double bondscreated by hydrogenating process (adding Hydrogen) Workhorses of cells, doing a variety of tasks such as communication, structure, movement, storage, transport, defense and enzymes Monomer: amino acids (20 amino acids exist in living things, distinguished by their R groups) ◦ have an amino end & a carboxyl end ◦ Some are hydrophobic, some hydrophilic, some positive, some negative, uncharged ◦ Held together by peptide bonds, and are therefore sometimes called polypeptides (special case of condensation(dehydration synthesis) where N is bonded to C) DRAW TWO DIFFERENT AMINO ACIDS IN YOUR NOTES. Circle the portion of the molecule they have in common. Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Alanine (Ala or A) Methionine (Met or M) Isoleucine (Ile or I) Leucine (Leu or L) Valine (Val or V) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Polar side chains; hydrophilic Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Electrically charged side chains; hydrophilic Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Basic (positively charged) Acidic (negatively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Forming a Peptide Bond: condensation (dehydration synthesis) O O H H H N C O H H N C O H H H Amino Acid Structure Peptide Bond O H O H H N C N C O H H H O H H Read instructions and record information on your “data sheet”. Do not paste this into your notebook until we finish notes. Pause after Step 4 to wrap up before you answer the ANALYSIS Questions. Primary structure=sequence of amino acids (read from amino terminus to carboxyl terminus) Secondary structure=coiling or folding of the molecule b/c of hydrogen bonds between backbone molecules (therefore, these are regular ex: alpha helices and pleated sheets) Tertiary structure=contortion of the molecule due to attractions (van der Waals and H bonding) between R groups. Because each protein has a unique AA sequence, these are irregular patterns that are unique to each protein (ex=disulfide bridges between sulfhdryl groups, hydrophobic clustering) Quaternary structure=overall protein structure resulting from multiple polypeptides (ex=hemoglobin has 4 polypeptide chains Primary structure Amino acids Amino end Primary structure of transthyretin Carboxyl end Tertiary structure Secondary structure Quaternary structure helix Hydrogen bond pleated sheet strand Hydrogen bond Transthyretin polypeptide Transthyretin protein Sickle-cell hemoglobin Normal hemoglobin Primary Structure 1 2 3 4 5 6 7 Secondary and Tertiary Structures Quaternary Structure Function Molecules do not associate with one another; each carries oxygen. Normal hemoglobin subunit Red Blood Cell Shape 10 m 1 2 3 4 5 6 7 Exposed hydrophobic region Sickle-cell hemoglobin subunit Molecules crystallize into a fiber; capacity to carry oxygen is reduced. 10 m High temperature, extreme salinity and pH changes can cause denaturating of proteins= protein becomes misshapen because the forces controlling the levels of structure have been altered Information storage molecules DNA and RNA Monomers are nucleotides. ◦ Phosphate Group ◦ Sugar (deoxyribose in DNA, ribose in RNA) ◦ Nitrogenous base (purines=A and G pyrimidines=T, C, and U) that bond purine to pyrimidine based on the number of H-bonds each has the ability to make Sequences are the code for creating proteins. Sequence changes are used as Biological Clocks. Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Sugars Purines Adenine (A) Guanine (G) (c) Nucleoside components Deoxyribose (in DNA) Ribose (in RNA) Metabolism is the sum total of all Anabolic (putting together) and Catabolic (taking apart) chemical reactions in the body Basic Cellular energy molecule fueling metabolism is ATP (adenosine triphosphate) Enzymes are proteins Catalyst=changes the rate of the reaction but is not consumed (used up) by the reaction Enzymes lower the activation energy of the reaction (activation energy or free energy of activation is usually in the form of heat and is required to make the molecules interact or break) Add Diagram #1 to notes. ◦ Highlight the original reaction in RED and the enzyme aided reaction in GREEN. ◦ Circle the ONE portion of the graph (rxn) that is changed by the addition of an enzyme. Free energy Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants G is unaffected by enzyme Course of reaction with enzyme Products Progress of the reaction Enzymes are specific to their substrate (reactant) because the shape of the active site (only region of enzyme that binds to substrate) conforms to the shape of the substrate (induced fit) Like a clasping handshake or lock & key Diagram #2: Use the following picture or find a picture in the text or online that represents this concept. Draw into your notes. 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower EA and speed up a reaction. 6 Active site is available for two new substrate molecules. Enzyme 5 Products are released. 4 Substrates are converted to products. Products 1. Bitesize Digestion: https://www.youtube.com/watch?v=eSbmJPSnw Bs 1. Denaturation occurs in enzymes due to pH, temperature, salinity changes. Paste Diagram #3 into your notes. Think of test questions for these graphics. 2. Concentration of Enzyme/Concentration of Substrates 3. Cofactors or coenzymes=non-substrate attachments to the enzyme that help maintain shape (allosteric) ◦ Ex: vitamins 4. Inhibitors Competitive=mimics the substrate and blocks the active site Non-competitive=causes inhibition by destabilizing the enzyme shape (allosteric) Ex: toxins & poisons Paste Diagrams #4 and #5 into your notes. (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor 5. Cooperativity=enzymes can have multiple active sites, so induced fit at one active site may cause stabilization of other active sites on the enzyme (b) Cooperativity: another type of allosteric activation (a) Allosteric activators and inhibitors Allosteric enzyme with four subunits Active site (one of four) Regulatory site (one of four) Substrate Activator Inactive form Stabilized active form Active form Oscillation Nonfunctional active site Inactive form Inhibitor Stabilized inactive form Stabilized active form Series of chemical reactions in which the products of each step are reactants for the next step Active site available Isoleucine used up by cell Active site of Feedback enzyme 1 is inhibition no longer able to catalyze the conversion of threonine to intermediate A; pathway is switched off. Isoleucine binds to allosteric site. Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A Enzyme 2 Intermediate B Enzyme 3 Intermediate C Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine) Read the article and discuss it at your table. Use one of the dry erase boards to map the enzymes, substrates and processes involved in creating grey hair and preventing grey hair. Put your initials on the board so it can be checked.