Mrs C’s Chem Lecture

H bonds: weak attraction between polar covalent molecules Van der Waals: very weak attraction between nonpolar covalent molecules (even molecules themselves)

Fig (a) Structures of endorphin and morphine (b) Binding to endorphin receptors Natural endorphin Endorphin receptors Morphine Brain cell Morphine Natural endorphin Carbon Hydrogen Nitrogen Sulfur Oxygen STRUCTURE = FUNCTION Molecular Shape -crucial in biology Determines: - Recognition - Specific responses Morphine and heroin (opiates) - Mimic brain’s endorphins - Affect pain perception and emotional state

Fig. 4-2 Water vapor H2H2 NH 3 “Atmosphere” Electrode Condenser Cold water Cooled water containing organic molecules Sample for chemical analysis H 2 O “sea” EXPERIMENT CH 4

Fig. 4-8 Drug Ibuprofen Albuterol Condition Pain; inflammation Asthma Effective Enantiomer S-Ibuprofen R-Albuterol R-Ibuprofen S-Albuterol Ineffective Enantiomer

Fig. 4-7 Pentane (a) Structural isomers (b) Geometric isomers 2-methyl butane cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (c) Enantiomers L isomer D isomer

Fig. 4-10c STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Carboxyl Acetic acid, which gives vinegar its sour taste Carboxylic acids, or organic acids Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). Acetic acidAcetate ion

Fig. 4-10d STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Amino Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Amines Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms). Ionized, with a charge of 1+, under cellular conditions. (ionized)(nonionized) Glycine

Fig. 4-10e STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Sulfhydryl (may be written HS—) Cysteine Cysteine is an important sulfur-containing amino acid. Thiols Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. 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, then breaking and re-forming the cross-linking bonds.

Fig. 4-10f STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Phosphate In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. Glycerol phosphate Organic phosphates Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Has the potential to react with water, releasing energy.

Fig. 4-10g STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Methyl 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. 5-Methyl cytidine Methylated compounds Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function.

Fig. 5-5 (b) Dehydration reaction in the synthesis of sucrose GlucoseFructose Sucrose MaltoseGlucose (a) Dehydration reaction in the synthesis of maltose 1–4 glycosidic linkage 1–2 glycosidic linkage

Fig. 5-6 (b) Glycogen: an animal polysaccharide Starch Glycogen Amylose Chloroplast (a) Starch: a plant polysaccharide Amylopectin Mitochondria Glycogen granules 0.5 µm 1 µm

Liver: Glucagon causes breakdown of glycogen into glucose Glucose ATP triglyceride glycogen liver muscles

Fig. 5-7 (a)  and  glucose ring structures  Glucose  Glucose (b) Starch: 1–4 linkage of  glucose monomers(b) Cellulose: 1–4 linkage of  glucose monomers

Fig Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol)

Fig Structural formula of a saturated fat molecule Stearic acid, a saturated fatty acid (a) Saturated fat Structural formula of an unsaturated fat molecule Oleic acid, an unsaturated fatty acid (b) Unsaturated fat cis double bond causes bending

Fig (b) Space-filling model (a)(c) Structural formula Phospholipid symbol Fatty acids Hydrophilic head Hydrophobic tails Choline Phosphate Glycerol Hydrophobic tails Hydrophilic head

Fig Hydrophilic head Hydrophobic tail WATER

Table 5-1

Fig Enzyme (sucrase) Substrate (sucrose) Fructose Glucose OH H O H2OH2O

Fig. 5-UN1 Amino group Carboxyl group  carbon

Fig Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Trypotphan (Trp or W) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged AcidicBasic Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

Peptide bond Fig Amino end (N-terminus) Peptide bond Side chains Backbone Carboxyl end (C-terminus) (a) (b)

Fig Primary Structure Secondary Structure Tertiary Structure  pleated sheet Examples of amino acid subunits + H 3 N Amino end  helix Quaternary Structure

Fig. 5-21f Polypeptide backbone Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Hydrogen bond

Fig. 5-21g Polypeptide chain  Chains Heme Iron  Chains Collagen Hemoglobin

Fig Primary structure Secondary and tertiary structures Quaternary structure Normal hemoglobin (top view) Primary structure Secondary and tertiary structures Quaternary structure Function  subunit Molecules do not associate with one another; each carries oxygen. Red blood cell shape Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 10 µm Normal hemoglobin     Val His Leu ThrPro Glu Red blood cell shape  subunit Exposed hydrophobic region Sickle-cell hemoglobin   Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.   Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 10 µm Sickle-cell hemoglobin GluPro Thr Leu His Val

Fig. 5-22c Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen. Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 10 µm

Fig Hollow cylinder Cap Chaperonin (fully assembled) Polypeptide Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein

V max: slope of the steepest part of the line When comparing different rates use the steepest line = constant rate of change

Q10 : a measurement of a rate of a chemical reaction and its relationship to temp. TempmL 4 C2 14 C4 Q10=2 R : rate of reaction = slope of the line Q10 calculator

What are the costs and benefits of being an Ectotherm (poikilotherm) or endotherm (homeotherm Q10 Effect = Rates for most enzyme mediated reactions increase by a factor of 2-3 for 10 degree temp increases

Fig. 5-UN3 % of glycosidic linkages broken Time ~ constant rate : not enough products to collide with active site - Assume substrate is in excess Rxn rate = slope of linear portion of the curve

Enzyme lab prelab What is catalase? Where is it found? –Organs, aerobes, anaerobes, animals, plants… What does it do? Why do we have it? Research function of the liver and kidney, potatoes and green plants in relation to catalase.

Enzymatic Activity cont Draw a diagram(s) and label the following terms with brief explanations: –Active site –Allosteric site –Feedback inhibition (find a loop) Draw idealized graphs for enzymatic activity for pH, temp, concentration and ion concentration

Procedure Scenarios Temp, catalase sources Diagrams Steps (why do you need each step?) Data tables Graphs