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Lecture 3


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McMaster University
Lovaye Kajiura

1 WEEK 3: MONDAY, SEPTEMBER 16 THTO FRIDAY, SEPTEMBER 20 , 2013 CHAPTER 3: BIOLOGICAL MOLECULES & SUPPLEMENTARY INFORMATION Figure 3-1 Bonding Patterns - The bonding patterns of the four most common atoms in biological molecules. A single line indicates a single covalent bond (two shared electrons) with another atom. Two parallel lines indicate a double covalent bond (four shared electrons), a three parallel lines indicate a triple covalent bond (six shared electrons) between the atom shown and another atom. Biological Molecules - Organic describes molecules that have a carbon backbone bonded to hydrogen atoms (derived from organisms to synthesize and use this general type of molecule). Inorganic molecules lack carbon atoms (example are water and salt) or lack of hydrogen atoms (carbon dioxide); far less diverse -Four most common types of atoms found in biological molecules are hydrogen, carbon, nitrogen, oxygen -Functional groups (attached to backbone of organic molecules) commonly occurring combinations of atoms; seven example are shown in table 3-1; Functional groups are less stable than the carbon backbone and more likely to participate in chemical reactions, and so they are mainly responsible for the properties and chemical reactivity of organic molecules. Table 3-1 Important Functional Groups in Biological Molecules FUNCTIONAL GROUPS Group Structure Properties Found In Hydroxyl -O-H Polar; involved in dehydration Sugars, and hydrolysis reactions; polysaccharides, nucleic forms hydrogen bonds acids, alcohols, some amino acids, steroids Carbonyl Polar; makes parts of Sugars (linear forms), molecules hydrophilic (water steroids hormones, soluble) some vitamins Carboxyl Polar and acidic; the Amino acids, fatty acids, negatively charged oxygen carboxylic acids (such may bond a third H+, forming as acetic and critic carboxylic acid (-COOH); acids) involved in peptide bonds Amino Polar and basic; may become Amino acids, nucleic ionized by binding a third H+' acids, some hormones involved in peptide bonds Sulfhydryl Nonpolar; forms disulfide Phospholipids, bonds in proteins nucleotides, nucleic acids 2 Phosphate (ionized Polar and acidic; links Steroids, methylated form) nucleotides in nucleic acids; nucleotides in DNA forms high energy bonds in ATP (ionized form occurs in cells) HYDROGEN, HYDROXYL (alcohols), CARBOXYL (carboxylic acids), CARBONYL (aldehydes, ketones) Aldehyde (ex. Propanol), Ketone (ex. Acetone), AMINO (amines), SULFHYDRYL – thiols, PHOSPHATE (organic phosphates), METHYL - CH ALSO, 3, ADDITIONAL functional group: ACETYL - COCH 3 Why are FUNCTIONAL GROUPS IMPORTANT? -each functional group imparts specific chemical properties ^^^ Figure 3-2 Dehydration Synthesis = condensation reaction - a hydrogen ions is removed from one subunit and a hydroxyl ion is removed from a second subunit leaving openings in the outer electron shells of atoms in the two subunits -openings are filled when the subunits share electrons creating covalent bond that links them Figure 3-3 Hydrolysis * -larger to smaller, breaking down -reverse reaction; breaks apart the molecule into its original subunits w/ water donating a hydrogen ion to one subunit and a hydroxyl ion to another (breaks down food) Table 3-2 Principle Types of Biological Molecules Type and Structure of Principal Subtypes and Examples Molecule Structures Carbohydrate: primarily Monosaccharide: Simple Glucose, fructose, galactose carbon, oxygen, and hydrogen, sugar, often with the formula C6 in the approximate formula H12 O6 Sucrose (CH2O)* Disaccharide: Two monosaccharides bonded Starch, glycogen, cellulose together Polysaccharide: Chain of monosaccharides (usually glucose) Lipid: Contains a high Triglyceride: three fatty acids Oil, Fat proportion of carbon and bonded to a long chain alcohol hydrogen; most lipids are Wax: Variable numbers of fatty Wax in plant cuticle nonpolar and in soluble in water acids bonded to a long chain alcohol 3 Phospholipid: Polar phosphate Phospholipids in cell group and two fatty acids membranes bonded to glycerol Steroid: Four fused rings of carbon atoms with functional Cholesterol, estrogen, groups attached testosterone Protein: Consists of one or Peptide: Short Chain of amino Oxytocin more chains of amino acids; acids Hemoglobin, keratin may have up to four levels of Polypeptide: Long chain of structure that determine its amino acids function Nucleotide/Nucleic acid: Nucleotide: Composed of five- Adenosine triphosphate (ATP) carbon sugar (ribose or cyclic adenosine deoxyribose) a nitrogen- monophosphate (cAMP) containing base, and a phosphate group Deoxyribonucleic acid (DNA), Nucleic acid: A polymer of ribonucleic acid (RNA) nucleotide subunits joined by covalent bonds between their phosphate and sugar groups Structure, Function, Significance CARBOHYDRATES - molecules are composed of carbon, hydrogen and oxygen in the approx. Ratio 1:2:1 (Carbohydrates literally translates to “carbon plus water”). All carbs are either small, water soluble sugars or polymers of sugar as starch. If a carb consists of one sugar it is called a monosaccharide, two sugars is a disaccharide. A polymer of many monosaccharides is called a polysaccharide. Most do not dissolve in water at body temperatures. Starches are polysaccharides that serve as energy storage molecules in cells. Other polysaccharides strengthen the cell walls of plants, fungi and bacteria, or form a supportive armor over the bodies of insects, crabs and their relatives. EXAMPLE: Plant cell MONOSACCHARIDES -single, simple sugars -Ribose (RNA) & Deoxyribose (DNA) -Glucose (starch, Cellulose, Glycogen) -Galactose (Cartilage) Figure 3-5 Depictions of glucose structure PG. 38 a) Chemical formula b) Linear and ball stick c) Ring, ball and stick d) Ring, simplified 4 Figure 3-6 Some six-carbon monosaccharides ** Figure 3-7 Some five-carbon monosaccharides ** ribose, deoxyribose DISACCHARIDES -double sugars that consist of two monosaccharides -which are joined a dehydration synthesis (condensation reaction) -often used for short term storage (in plants) Ex. Glucose + Glucose = Maltose -Sucrose Figure 3-8 Synthesis of a disaccharide -Sucrose is synthesized by a dehydration reaction in which a hydrogen is removed from glucose and a hydroxyl group is removed from fructose. This forms a water molecule and leaves the two monosaccharide rings joined by single bonds to the remaining oxygen atom. POLYSACCHARIDES -are chains of monosaccharides -Plants often use starch as an energy-storage molecule -Animals often store glycogen, a similar polysaccharide -Starch & Glycogen are polymers of glucose molecules -Starch commonly formed in roots and seeds consists of branched chains of up half a million glucose subunits. Glycogen stored in the liver and muscles of animals (including people) is also a chain of glucose subunits but is more highly branched than starch -Many organisms use polysaccharides as structural materials; Most important structural polysaccharides is cellulose which makes up the walls of living cells of plants (Plants synthesize about a trillion tons of cellulose each year making it the most abundant organic molecule on Earth) -Cellulose is a polymer of glucose, but every other glucose is “upside down” -Cows, termites, harbor cellulose-digesting microbes in their digestive tracts and can benefit from glucose subunits the microbes release. -In humans, cellulose fibers pass intact through the digestive system supplying no nutrients but providing the “roughage” that helps prevent constipation -Supportive coverings of insects, crabs, spiders are made of chitin, a polysaccharide in which the glucose subunits bear a nitrogen containing functional group. Also stiffens the cell walls of many fungi, including mushrooms. -Carbs. May also form parts of larger molecules; for example, the plasma membrane that surrounds each cell is studded with proteins to which carbs are attached. Nucleic acids also contain sugar molecules
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