Carbon. Carbon. Carbon Skeleton 8/25/2016. The Chemical Building Blocks of Life

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1 The Chemical Building Blocks of Life Carbon Life as we know it is carbon-based. Biological molecules are built on a carbon skeleton. Small atom with a valence of 4. Carbon Can form up to 4 covalent bonds. Can form double bonds. molecules containing carbon can form straight chains, branches, rings, balls, tubes and coils. Frequently bonds with carbon, hydrogen and oxygen. Also with nitrogen, sulfur, and phosphorus. Molecules with lots of carbon-hydrogen bonds are called: Hydrocarbons. Carbon Skeleton Chains of carbon atoms that form the backbone of organic compounds. 1

2 a group of atoms responsible for the characteristic reactions and properties of a particular compound. Attach to the carbon skeleton. Ex: Amino group Functional Groups Carbon Skeleton + Functional Groups Any carbon skeleton + a functional group = a biological macromolecule. Types of biological macromolecules: carbohydrates nucleic acids proteins lipids These are the structural materials of all living things. Macromolecule Big molecule. Very long molecule made of the same repeating type of building block. A long repetitive molecule is called a polymer. The building block that repeats is called a monomer. 2

3 How to build polymers Dehydration reactions. Removing water. Remove one H from one part and one OH from the next part. Then put them together, leaving H 2 O leftover. How to break apart polymers Hydrolysis reaction. Adding water. Insert H 2 O. The H goes with one piece and the OH goes with the other piece. Breaks apart. Key mechanism in digestion. 3

4 Carbohydrates Molecules with a 1:2:1 ratio of carbon, hydrogen, oxygen. Empirical formula (CH 2 O) n C H covalent bonds hold much energy. Carbohydrates are good energy storage molecules. Examples: sugars, starch, glucose, cellulose. Energy-packed compounds. Energy is used quickly and must be constantly replenished. 22 Functional Groups in Carbohydrates Carbohydrates Evil or not evil? Depends on how fast it burns. Vegetable fiber is a carb and so is frosting. 4

5 Types of Carbohydrates Monosaccharides Simple sugars consisting of three to seven carbon atoms. Hydroxyl groups (-OH) and Carbonyl groups (-O=C-). Exist as a straight chain molecule, but in solution (cells!) they form rings. Glucose Most common monosaccharide is glucose. Glucose is important for energy storage. Disaccharides Di means two. Two simple sugars combined. Reservoirs of glucose. Connecting bond broken down by enzymes at destination. Disaccharides are formed by dehydration synthesis. 5

6 Oligosaccharides More than two sugars, but just a few form short chains. Important markers and receptors on the outside of cells. Polysaccharides Poly means many. Long, very long, and super long chains of sugars. Some can have thousands of monosaccharide sugars strung together. Examples: starch and cellulose. Cellulose Long fibersthat are very strong. Resistant to metabolic breakdown. Made of glucose units. Starch Insoluble polysaccharides. Long chains that tend to coil up in solution. This coil makes them insoluble. In plants: amylose and amylopectin. In animals: glycogen provides a similar function to starch. 6

7 Chitin Structural material found in arthropods that makes the exoskeleton. Polysaccharide cross-linked by proteins. Very tough material. Proteins Very diverse. Can t cover them all. Most jobs in a cell are performed by proteins. Seven general categories of function: 1. Enzyme catalysts 2. Defense 3. Transport 4. Support/structure 5. Motion 6. Regulation 7. Storage Proteins Monomer: Amino Acid Polymer: Polypeptide 20 different amino acids. Amino acids form long chains called polypeptides. One or more polypeptides = a protein. 7

8 Amino acids joined by dehydration synthesis Peptide bond 4 Levels of Structure The shape of a protein determines its function. Protein shape is complex and is essential to protein function. Must fold or coil to function. Levels: Primary Secondary Tertiary Quaternary 43 How Proteins Fold or Coil Hydrogen bondsform between atoms in the backbone of the polypeptide chain because the amino acids form polar groups. The N-H and the C=O in the amino groups are joined with polar covalent bonds. 4 Levels of structure: Primary 1.Primary structure sequence of amino acids 4 Levels of structure: Secondary 1.Secondary structure interaction of groups in the peptide backbone αhelix βsheet

9 4 Levels of structure: Tertiary 3. Tertiary structure final folded shape of a globular protein. Final level of structure for proteins that consist of only a single polypeptide chain. 4 Levels of structure: Quaternary 3. Quaternary structure arrangement of individual chains (tertiary subunits) in a protein with 2 or more polypeptide chains Additional structural characteristics Motifs Common elements of secondary structure seen in many polypeptides Useful in determining the function of unknown proteins Domains Functional units within a larger structure Most proteins made of multiple domains that perform different parts of the protein s function Chaperones Chaperone proteins help protein fold correctly, refold if damaged, or tag for disposal

10 Denaturation Protein loses structure and function Due to environmental conditions ph Temperature Ionic concentration of solution 56 Enzymes: A type of protein Enzymes are catalysts: molecules that speed up chemical reactions. Without enzymes, cellular reactions wouldn t happen fast enough for the cell to survive. Cells can regulate their chemistry by regulating enzymes. Nucleic Acids Large complex macromolecules that carry information, especially genetic information and protein production. Two main types of nucleic acid: DNA and RNA DNA: deoxyribonucleic acid RNA: ribonucleic acid Can produce copies of themselves. Monomer: nucleotide Polymer: nucleic acid Nucleic Acids A nucleotide is made of: sugar + phosphate + nitrogenous base sugar is deoxyribose in DNA or ribose in RNA Nitrogenous bases include Purines: adenine and guanine Pyrimidines: thymine, cytosine, uracil 10

11 Nitrogenous bases Pyrimidines (cytosine, thymine, uracil) have a single ring structure with two nitrogen atoms in the ring. Purines (adenine and guanine) have two fused rings with two nitrogen atoms within each ring. 61 Deoxyribonucleic acid (DNA) Encodes informationfor the amino acid sequence of protein formation and genetic information. Double helix 2 polynucleotide strands connected by hydrogen bonds. Twisted ladder structure. Sides of the ladderare made of sugar and phosphate components. The steps or rungs of the ladder are made of nitrogenous bases. Bases pairs: A with T, C with G (one purine with one pyrimidine in a hydrogen bond)

12 Ribonucleic acid (RNA) RNA is produced by transcription (copying) from DNA. Single-stranded (most of the time). Three types: 1. Messenger RNA (mrna) carries code for protein structure from DNA to ribosomes where protein is made. 2. Transfer RNA (trna) decodes the message in mrna. 3. Ribosomal RNA (rrna) is part of the structure of the ribosome. New Discoveries in RNA function Found to function as an enzyme: catalytic RNA. Newly discovered forms of RNA are involved in regulating gene expression. sirna: small inhibitory RNA mirna: microrna These small bits of non-coding RNA target mrna for destruction and regulate gene expression. 69 Lipids Hydrophobic and insoluble in water. High energy density long term energy storage. Nonpolar molecules. Can t fold up like proteins, so long lipid chains spontaneously cluster together in water (solution). Forms cellular membranes. Monomer: glycerol and fatty acids. Polymer(sort of): lipid. Lipids Major types: Fats and oils (triglycerides) Phospholipids Waxes Sterols (steroids and hormones) 12

13 Triglyceride Structure Triglyceride structure: Glycerol backbone with three fatty acid chains attached. Fats and Oils Saturated: Carbon atoms are bonded to each other with single bonds and with two hydrogen atoms. Forms straight, tightly packed chains. From animals. Unsaturated: Carbon bonds with some double bonds, which in turns means only one hydrogen. Forms kinks in the chain. From plants. Monounsaturated: one double carbon bond. Polyunsaturated: more than one double bond. Saturated and Unsaturated Fats Partially Hydrogenated Fats Hydrogenated means making more bonds with hydrogen. Why? Increases shelf-life. Takes longer to go rancid. 13

14 Waxes Formed from fatty acids and long chain alcohols. Very long carbon chains with lots of nonpolar carbon hydrogen bonds. Sterols Steroids and hormones. Four fused carbon rings with lots of nonpolar carbon hydrogen bonds. Examples: testosterone, estrogen, cholesterol, vitamin D. Phospholipids Type of complex lipid that forms biological membranes. Have a polar hydrophilic head and two nonpolar hydrophobic tails. Amphipathic. This causes the tails to cluster together in water and the head to point outward. Structure: Glycerol head Two fatty acid tails 14

15 Micelles lipid molecules orient with polar (hydrophilic) head toward water and nonpolar (hydrophobic) tails away from water Phospholipidbilayer more complicated structure where 2 layers form Hydrophilic heads point outward Hydrophobic tails point inward toward each other You say fat like it s a bad thing! Some functions of lipids: Insulation in animals. Protects from the cold. Shock-absorbing layer around vital organs. Insulates nerve cells. Makes biological membranes. Waxes are water-proofing: plant leaves, bird feathers. Signaling in the body by steroid hormones