Week 5 Biomolecules Lecture Notes PDF

Molecular Biology BIOM 411 Week 5. Biomolecules Over the next few lectures we’ll discuss … Organic Molecules and Polymers Biological Macromolecules Membrane Structure & Function  Does the structure and composition of molecules really make a difference? Does the structure and com...

Molecular Biology BIOM 411 Week 5. Biomolecules Over the next few lectures we’ll discuss … Organic Molecules and Polymers Biological Macromolecules Membrane Structure & Function  Does the structure and composition of molecules really make a difference? Does the structure and composition of molecules really make a difference? The importance of Functional Functional groups are chemical groups that … contribute to function by affecting the molecule’s shape affect molecular function by being directly involved in chemical Most important reactions functional groups for biology 1. Hydroxyl -OH 2. Carbonyl >CO 3. Carboxyl -COOH 4. Amino -NH2 5. Sulfhydryl -SH 6. Phosphate -PO32- 7. Methyl -CH3  Each functional group participates Chemical Building Blocks of Life Four Major Types of Biological Molecules: 1. Lipids 2. Nucleic Acids 3.Proteins 85% of the cell 4.Carbohydrates Four Major Types of Biological Molecules: 1.Lipids = phospholipids have amphipathic properties important for membrane dynamics 2.Nucleic Acids = polymers of nucleotides in the form of either DNA or RNA (second most abundant macromolecule in a cell) 3.Carbohydrates = polymers of sugars found in the cell wall and also used for Carbon source. 4.Proteins = polymers of amino acids, with structural and enzymatic roles in the cell (most abundant macromolecule in a cell!) Many giant macromolecules in the body are polymers. Polymers are molecules composed of a repetitive series of identical or similar units called monomers. ex starch is polymer glucose is monomer to make starch Joining monomers together is called polymerization, and is accomplished by dehydration synthesis or condensation. Build ‘em up! The synthesis of polymers (“polymerization”) occurs when 2 monomers are covalently bonded to each other and there is the loss of a water molecule. This process is called a condensation reaction or dehydration synthesis. The dehydration process is facilitated by specific enzymes (proteins that speed up the chemical reaction). Break ‘em down! Polymers disassemble into monomers by hydrolysis, “to break using water”, which is the reverse of the dehydration reaction. Just remember … “Break a water, break a HO 1 2 3 H HO H Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond H2O HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 H HO H Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond H2O HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 4 H Hydrolysis adds a water H2O molecule, breaking a bond HO 1 2 3 H HO H (b) Hydrolysis of a polymer Carbohydrates  Carbohydrates are sugars and polymers of sugars monosaccharides = simple sugars disaccharides = two monosaccharides joined by a dehydration synthesis reaction polysaccharides = many sugar building blocks joined together Carbohydrates have a general formula of a multiple of CH2O. Monosaccharides: Disaccharides: - Simple sugars, like - 2 sugars joined by “glycosidic glucose! linkage” during the dehydration - Major nutrient/fuel source reaction for cellular work - Sucrose = glucose + fructose - When not used -Lactose (in milk) = glucose + immediately, then stored as galactose di- or polysaccharide - Maltose = glucose + glucose  Trioses (C3H6O3) Pentoses (C5H10O5) Hexoses (C6H12O6) Aldoses Glyceraldehyde Ribose Glucose Galactose Ketoses Dihydroxyacetone Ribulose Fructose Dehydration synthesis = linking things together, but losing a water molecule Polysaccharides are macromolecules with hundreds to thousands of monosaccharides joined by glycosidic linkages! Polysaccharides are used for storage or structural purposes. The function of the polysaccharide is determined by its sugar monomers and position of its glycosidic linkages. Storage: Plants = starch is a polymer of glucose molecules (as granules within cellular structures) so the plant can stockpile extra glucose as stored energy Animals = glycogen is a polymer of glucose stored mostly in the liver and muscles (these reserves don’t last long in humans!) (a)  and  glucose ring structures  Glucose  Glucose (b) Starch: 1–4 linkage of  glucose monomers (b) Cellulose: 1–4 linkage of  glucose monomers Fig. 5-6 Cell walls Cellulose microfibrils in a plant cell wall Microfibril 10 µm 0.5 µm Cellulose molecules b Glucose monomer Cellulose makes strong building material for plants. Who cares? Cellulose is the major constituent in paper! Cellulose is the ONLY constituent in cotton! So we use it, but do we eat it? … Sure! Enzymes that break down alpha linkages (like those in starch) cannot break down beta linkages (like those in cellulose). Humans do not have enzymes to break down cellulose, so it passes right on through our digestive tracts as “insoluble fiber” or “roughage”. Example: cows and termites and microbes – Lipids Lipid = hydrophobic organic molecule usually composed of only carbon, hydrogen, and oxygen Lipids are much less oxidized than carbohydrates, so they have more calories per gram! 5 primary types of lipids in humans: 1.Fatty acids – saturated, unsaturated and polyunsaturated (depends on double bonds!) 2.Triglycerides – three fatty acids covalently bonded to a glycerol 3.Phospholipids – similar to fats, but a phosphate group takes the place of one fatty acid. These are amphiphilic! 4.Eicosanoids – hormone-like chemicals that signal between cells  Saturated & Unsaturated Fats Saturated fatty acid - all C’s are single bonds, and all other available bonds are H’s (“saturated with H’s”) - made from saturated fatty acids = saturated fat - flexible tails allow fats to tightly pack together, so… solid at room temp - usually animal fats Unsaturated -one or more double bonds between C’s - made with unsaturated fatty acids = unsaturated fat - tails are more rigid, can’t pack together because kinks at cis double bonds … liquid at room temp Phospholipids … are essential for cells because they make up the cell membranes! = 2 fatty acids + glycerol +phosphate group So… One end is hydrophilic (glycerol + negatively charged phosphate group) One end is hydrophobic (2 long hydrocarbon fatty acid chains) “Amphipathic” = fits Notice how their “form having a hydrophilic region and a hydrophobic region function” These molecules will self assemble such that the hydrophilic heads orient toward water and the hydrophobic tails orient toward each other to exclude water. Proteins Proteins are made up of… polypeptides are made up of … amino acids linked together. Each amino acid composed of: 1. An amine group 2. A carboxyl group 3. A characteristic “side chain” We can group amino acids based on the properties of their side Many aa’s linked together = polypeptide We link aa’s (monomers) together by a dehydration reaction between aa1 hydroxyl group and aa2 amino group. The resulting covalent bond is called a peptide bond. Protein structure – see Figure 5.18 pages 80-81 Levels of protein structure: 1.Primary = amino acid sequence 2.Secondary = local twists that contribute to protein’s shape Alpha helix Beta pleated sheet 3.Tertiary = overall shape of a polypeptide resulting from folding interactions between side chains of aa’s far away Hydrophobic interactions Disulfide bridges 4.Quaternary = two or more polypeptide chains  Protein folding and unfolding Denaturation -occurs when conditions are unfavorable to support protein folding and stability (pH, salt concentration, temperature) - protein will unravel and lose its “native” shape = biologically inactive How does this happen in the cell? Chaperonins (“chaperone proteins”) facilitate protein folding by keeping the polypeptide safe Nucleic Acids: DNA & RNA How is the amino acid sequence of a polypeptide determined? … by a gene !! 2 types of Nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA genetic material passed from parent to offspring arranged into genes, many genes located together on a chromosome genes encode the information for all of the cell’s activities RNA some genes on a DNA molecule direct the synthesis of messenger RNA = “making a copy of a gene” then the mRNA conveys the genetic instructions to the DNA  RNA protein synthesis machinery Protein to make the protein at the ribosomes Nucleic Acids Store, transport, and control hereditary information Deoxyribonucleic acid = DNA Ribonucleic acid = RNA Nucleotides contain: 1.Sugar (ribose) 2.Phosphate 3.Nitrogenous  Ribose Sugar Phosphat e Base Is there a hydroxyl (-OH) on C2? “Guanine “Cytosine ” ” “Adenine”  Put them together by … “Guanine “Cytosine ” ” “Adenine”  Structure of nucleic acids Nucleic acids are macromolecules that exist as polymers So… the monomers are nucleotides Nucleotide = sugar + phosphate group + nitrogenous base Sugar: deoxyribose in DNA ribose in RNA Nitrogenous bases pyrimidine has a six-member ring of carbon and nitrogen cytosine (C), thymine (T), uracil (U) Nucleic Acids Store, transport, and control hereditary information Deoxyribonucleic acid = DNA Ribonucleic acid = RNA RNA: 1. One strand DNA: 1. Two strands 2. Antiparallel 3. Purine + Pyrimidine DNA exists as a double helix. The 2 strands are anti-parallel with the sugar-phophate backbones running in opposite 5’  3’ directions (sugar-phosphate backbones on the outside, bases toward the middle) The bases pair: A = T (with 2 hydrogen bonds) G = C (with 3 hydrogen bonds) So, the two strands are complementary, each the predictable counterpart of the other one. That means, If one strand is … 5’– AGGTCCG –3’ Then the other strand is … 3’– TCCAGGC –5” Can you describe the … Structure of nucleic acids? Structure of nucleic acids Antiparallel … two lanes each going opposite directions Double helix Two (antiparallel) DNA strands connected in the middle by nitrogenous bases