Chapter 3 - Lecture Notes - PDF

Chapter 3 The Chemical Basis of Life II: Organic Molecules  Group Work Which of these is a pure hydrocarbon and what features of the molecule are you examining to make your choice? Which molecule(s) are fully nonpolar molecule and which one(s) is/are “amphipathic?” 3.1 The Carbon Atom...

Chapter 3 The Chemical Basis of Life II: Organic Molecules  Group Work Which of these is a pure hydrocarbon and what features of the molecule are you examining to make your choice? Which molecule(s) are fully nonpolar molecule and which one(s) is/are “amphipathic?” 3.1 The Carbon Atom and Carbon-Containing Molecules Section 3.1 Learning Outcomes 1. Explain the properties of carbon that make it the chemical basis of all life 2. Describe the variety and Loading… chemical characteristics of common functional groups of organic compounds 3.1 The Carbon Atom and Carbon-Containing Molecules Carbon Is an Essential Element for Life Organic molecules contain carbon - - Carbon has 4 electrons in its outer valence shell It needs 4 more electrons to fill - - the valence shell Can form up to four covalent - bonds This is the max # of bonds any - atom can make Carbon Carbon is a “scaffold” atom, aka Atom the backbone or chain of a lot of biological molecules 3.1 The Carbon Atom and Carbon-Containing Molecules Carbon Is an Essential Element for Life Carbon can form polar or nonpolar covalent bonds, depending on the electronegativity of the bonding partner Pure Hydrocarbons are nonpolar molecules containing a carbon backbone Have only C-C and C-H bonds Examples of molecules Hydrophobic and poorly soluble in water that are pure HYDROCARBONs. Notice the symmetry Loading… of these molecules. They do not have polar regions that are positive or negative. These repel water, but aggregate together (like oil in water) 3.1 The Carbon Atom and Carbon-Containing Molecules Carbon Is an Essential Element for Life Oxygen and nitrogen form polar bonds with carbon Partial Hydrocarbons have a carbon backbone, but are hydrophilic and soluble in water But many molecules in Biological organisms δ- are Partial Hydrocarbon Polar Hydrocarbons. “chain” “functional Notice the δ- δ+group” asymmetry of this molecule. IT DOES have polar regions that are positive or negative. These attract water through attraction of pos/neg charges. 3.1 The Carbon Atom and Carbon-Containing Molecules Carbon Atoms May Be Arranged into Functional Groups A functional group is a small group of atoms with specific chemical properties & consistent behavior in chemical reactions. Why do we care about them? Because they can completely change the function and solubility of the hydrophobic molecule to which they are attached. Functional group Ethane Ethane yields 20,630 BTUs Ethanol only yields 11,587 BTUs per per pound when combusted in pound when combusted an engine. Ethanol will dissolve in water. Ethane does not dissolve in water. 3.1 The Carbon Atom and Carbon-Containing Molecules Carbon Atoms May Be Arranged into Functional Groups A functional group exhibits similar chemical properties in all molecules in which it occurs 3.1 The Carbon Atom and Carbon-Containing Molecules Carbon Atoms May Be Arranged into Functional Groups A functional group exhibits similar chemical properties in all molecules in which it occurs 3.2 Synthesis and Breakdown of Organic Molecules Section 3.2 Learning Outcomes 1. Diagram how small organic molecules are assembled into larger ones by dehydration reactions and how hydrolysis reactions can reverse this process  3.2 Synthesis and Breakdown of Organic Molecules Imagine you are popping these beads together. Each bead is a monomer. The chain you make is called polymer. Polymers are formed by dehydration reactions A molecule of water is removed each time a new monomer is added; the process repeats to form long polymers Dehydration reactions are catalyzed by enzymes Loading… 3.2 Synthesis and Breakdown of Organic Molecules When you pull the beads apart it is called a hydrolysis reaction. A molecule of water is added back each time a monomer is released; the process repeats to break down a long polymer Hydrolysis reactions are catalyzed by enzymes The Molecules of life are polymers!  Let’s practice Formation of polymers from monomers typically involves ) removal of a molecule of water ) addition of a molecule of water ) a hydrolysis reaction ) a dehydration reaction )· both a and d 3.4 Carbohydrates Section 3.4 Learning Outcomes 1. Distinguish among different types of carbohydrate molecules, including monosaccharides, disaccharides, and polysaccharides 2. Relate the functions of plant and animal polysaccharides to their structure 3.3 Overview of the 4 Major Classes of Organic Molecules The 4 major classes of organic molecules are carbohydrates, lipids, proteins, and nucleic acids What structures are you familiar with that are composed of carbohydrates? 3.4 Carbohydrates Carbohydrates Monomer = monosaccharide Ring backbone containing carbons AND one oxygen atom Ring can be a pentose (5 sides) or hexose (6 sides) Bio 190 students needs to recognize and identify the molecular structure of a monosaccharide sugar when they see it 3.4 Carbohydrates Monosaccharides and Disaccharides Are Simple Carbohydrates dehydration reaction to form Monosaccharides can be joined together by a ______________ disaccharides Sucrose (table sugar) is a familiar disaccharide that is formed from glucose + fructose Lactose and maltose are also disaccharides The covalent bond formed between 2 sugars is called a glycosidic bond Disaccharides can be broken down through ____________ hydrolysis reactions Monosaccharides and disaccharides often function as an energy source 3.4 Carbohydrates Polysaccharides Are Carbohydrate Polymers Polysaccharides are formed when many monosaccharides are linked together; examples of polysaccharides include starch energy storage in plant cells glycogen energy storage in certain animal cells cellulose provides strength to plant cell walls peptidoglycans found in cell walls of certain bacteria chitin found in cell walls of fungi; found in exoskeletons of arthropods glycosaminoglycans found in connective tissues surrounding animal cells (ex: abundant in cartilage) · need to know ! 3.7 Nucleic Acids Section 3.7 Learning Outcomes 1. Describe the 3 components of a nucleotide 2. Distinguish between the structures of DNA and RNA 3. Explain how certain bases pair with others in DNA 3.7 Nucleic Acids Nucleotides Are the Building Blocks of DNA and RNA Nucleic acids are POLYMERS that are responsible for the storage, expression, and transmission of genetic information Two classes: Deoxyribonucleic acid (DNA) Stores genetic information encoded in the sequence of nucleotide monomers Ribonucleic acid (RNA) Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain 3.7 Nucleic Acids Nucleotides Are the Building Blocks of DNA and RNA Nucleotides are the monomer building blocks of nucleic acids Nucleotides are composed of three components: a phosphate group I a pentose sugar (ribose or deoxyribose) a nitrogenous base H50H - T * de = removal of oxygen ! Bio 190 students need to recognize the difference in the ribose sugar that differentiates a deoxyribonucleotide from a ribonucleotide. OHc. OH - Fig 3.21, Biology,  Brooker 3.7 Nucleic Acids Nucleotides Are the Building Blocks of DNA and RNA The nitrogenous bases in nucleotides: < 2 rings The purines, adenine (A) and guanine (G), have a ! double-ring structure Iring - The pyrimidines, cytosine (C) and thymine (T), have a single-ring structure remember : Dure As Gold "Cut pie" Py = pie tosine cut = Gracil thymine 3.7 Nucleic Acids DNA Is Composed of Two Strands That Form a Double Helix A DNA molecule consists of 2 strands of nucleotides, coiled around each other to form a double helix The strands are held together by hydrogen bonds that form between complementary “base pairs” A pairs with T C pairs with G ↑ DNAbase 3.7 Nucleic Acids RNA Is Usually Single Stranded Although they are generally similar, the structure of RNA differs in a few ways from the structure of DNA RNA is usually single stranded RNA nucleotides contain the sugar ribose RNA uses the nitrogenous base uracil in place of thymine -- DNA ! RNA ! 3.6 Proteins Section 3.6 Learning Outcomes 1. Give examples of the general functions that are carried out by different proteins 2. Describe how amino acids are joined to form a polypeptide 3. Diagram and explain the 4 levels of protein structure 4. Outline the factors that determine protein shape and function 5. Define protein domain 3.6 Proteins Proteins perform a variety of diverse functions in cells The MOST diverse molecule type 3.6 Proteins Amino Acids Are the Building Blocks of Proteins Proteins are polymers composed of 20 different amino acids - - www.bareblends.com  3.6 Proteins Amino Acids Are the Monomer of Proteins Each amino acid has a common core structure (list below) as well as a variable side chain (designated R) α-carbon I amino group carboxylic acid group hydrogen Loading… Carboxylic Acid functional group Muddy area in 190: Students have difficulties identifying the biological monomers. Examine the molecules here. They clearly are different, but you need some rules to describe those differences. Rules: A monosaccharide (sugar) contains a ring structure that includes carbons and ONE oxygen Nucleotides have 3 parts: phosphate group, sugar, base Amino acids do not have a ring and are named based on functional groups that they contain amino group, acid group "fist " "butterfly" "hang10" Discuss in your group WHY these rules work to “memorize” the monomer structures. If they don’t work for you, makeO' up your own rules. amiro acid nucleotide monosaccharise  3.6 Proteins Amino Acids Are the Building Blocks of Proteins The 20 amino acids are categorized by the chemical properties of the side chains; some R groups are polar while others are nonpolar ! Nonpolar (hydrophobic) amino acids: non-polar so ↑ no oxygen RECALL Activity: What - - + features make molecules non- + polar? Side chain = R-group = residue 3.6 Proteins Amino Acids Are the Building Blocks of Proteins Polar (hydrophilic) amino acids: RECALL Activity: What features oxygen make molecules polar? ↓ A polar be - 3.6 Proteins Proteins Have a Hierarchy of Structure or “Folding” Proteins structure is characterized at 4 progressive levels: Primary structure is the linear sequence of amino acids (encoded by genes); - peptide bonds contribute to primary structure - Secondary structure forms as some chemical groups (NH and CO) of the - backbone interact with each other via hydrogen bonds & interact +g α helices and β pleated sheets are common; turns and loops can also form as - - part of secondary structure Tertiary structure is the overall 3-dimensional folded shape of the protein; R - groups participate in chemical interactions and all types of bonds can potentially contribute to tertiary structure For some proteins, this is the final level of structure Quaternary structure occurs when - 2 or more protein subunits are assembled - together to form a functional complex; all types of chemical bonds can potentially contribute to quaternary structure - 3.6 Proteins Proteins Have a Hierarchy of Structure or “Folding” Quaternary Structure (2 or more proteins come together) Tertiary Structure (3-dimensional shape ) Secondary Structure (α helices & β pleated sheets ) Primary Structure (amino acids) 3.6 Proteins Proteins Have a Hierarchy of Structure or “Folding” Protein 3D Structure Is Determined by Several Factors More Acidic More Basic solution solution 1 7 H+ H+ 14 H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ The 1’ structure has H+ H+ not changed, but the H+ H+ H+ H+ H+ pH of the solution H+ H+ changed, and hence H+ H+ the 3’ structure H+ H+ H H++ H+ changed. H+ Food Hmash + travels H+ H+ from stomachH+(ph2) H+H+ H+ into intestine (pH H+ H+ H+ 8) H+ H+ H+ H+ 3.5 Lipids Section 3.5 Learning Outcomes 1. List the different classes of lipid molecules important in living organisms 2. Diagram the structure of a triglyceride, and explain how it is formed and how its structure is affected by the presence of saturated and unsaturated fatty acids 3. Explain why some fats are solid at room temperature and others are liquid 4. Discuss how triglycerides function as energy-storage molecules 5. Explain why 3.5 Lipids Lipids are composed predominantly of hydrogen and carbon atoms They do not have a monomer unit. A defining feature of lipids is that they are nonpolar and therefore very insoluble in water Lipids can be described as hydrophobic hydrocarbons Lipids are structurally diverse Carboxylic acid functional Fat or hydrocarbon part group 3.5 Lipids The Fatty Acid -long, linear carbon chain or backbone -carboxylic acid group at one end ↓ 3 representations of same lipid called a “fatty acid” Carboxylic acid functional Fat or hydrocarbon part group 1. 2. 3. Muddy area in 190: Students have difficulties identifying the biological monomers. Examine the molecules here. They clearly are different, but you need some rules to describe those differences. Rules: A sugar contains a ring structure that contains carbons and ONE oxygen Nucleotides contain 3 parts: phosphate group, sugar, base Amino acids do not have a ring and are named based on functional groups that they contain amino group, acid group Lipids have long (linear or ring) carbon backbones. 3.5 Lipids Type #1: Triglycerides are the molecules commonly known as fats and oils This is a stick structure drawing of a triglyceride. 3.5 Lipids Saturated fatty acids v Unsaturated fatty acids Carbons in the chain “saturated” with what? With H3 4 H Hydrogen atoms 1 2 Monounsaturated fatty acids contain one C=C, which introduces a kink into the shape Polyunsaturated fatty acids contain two or more C=C 3.5 Lipids Due to their straight structure, saturated fatty acids can pack together more tightly than unsaturated fatty acids Typical of animal fats that Typical of plant fats that are are solid at room temp liquid at room temp Considered “healthier” fats. For one reason is there is less fat contained per unit volume (aka, less calories per bite) 3.5 Lipids Type #2: Phospholipids compose the semi-permeable membrane surrounding ALL cells NEW term! The fatty tails attract each other side-by- side through “Hydrophobic interactions” 3.5 Lipids Type #3: Steroids contain Rings of carbon atoms Steroids have four interconnected rings of carbon atoms They are primarily composed of carbon and hydrogen and are usually insoluble in water © 2015 Pearson Education, Inc. 3.5 Lipids Type #4: Waxes Are Complex Lipids That Prevent Water Loss from Organisms Waxes are very, very long fatty acids Very nonpolar, thus they exclude water Waxes are used to protect organisms from water loss or as structural elements Ex: Waxy surface on leaves Ex: Beeswax in honeycombs