Lipids and Nucleic Acids PDF

The Chemical Basis of Life-6 ORGANIC MOLECULES: 3. Lipids and Nucleic Acids 1  Recap: Protein Structure… Primary Assembly STRUCTURE PROCESS Secondary...

The Chemical Basis of Life-6 ORGANIC MOLECULES: 3. Lipids and Nucleic Acids 1  Recap: Protein Structure… Primary Assembly STRUCTURE PROCESS Secondary Folding Tertiary Packing Quaternary Interaction 2  Lesson outcomes Discuss the different types of lipids Discuss nucleic acids 3 Lipids: Fats & Oils 4  Characteristics of Lipids Diverse group of organic compounds includes fats, oils, phospholipids, and cholesterol (steroids) composed of Carbon, Hydrogen, and Oxygen ratio of H:O greater than 2:1 building blocks are fatty acids and glycerol 5  Lipids Lipids are composed of C, H, O long hydrocarbon chains Do not form polymers larger molecules made of smaller subunits fat 6  Biological functions of Lipids Different kinds of lipids have different functions.. fats & oils - energy storage Fat – thermal insulation waxes & oils - Protective coatings and water barriers phospholipids - Structural and recognition components of cell membranes carotenoids - Accessories for acquisition of light in photosynthetic organisms Steroids & modified fatty acids - play a regulatory function as hormones and vitamins myelin – lipid coating around nerves = electrical insulation 7  Lipids Lipids are non-polar hydrocarbons = composed mainly of hydrogen and carbon insoluble in water Fats – solid at room temperature (20◦C) Oils – liquids at room temperature (20◦C) Fats & oils are triglycerides = 3 glycerides Triglyceride = 1 glycerol + 3 fatty acids Glycerol = a small molecule with 3 OH groups Fatty acid = long non-polar hydrocarbon chain and a polar carboxyl (COOH) group The fatty acids may be saturated or unsaturated. 8  Fatty Acid Structure Carboxyl group (COOH) forms the acid. “R” group is a hydrocarbon chain. 9 Fatty acid 10 Glycerol 11  Building Fats Triacylglycerol/triglyceride: 3 fatty acids linked to glycerol ester linkage = between OH & COOH formed by dehydration synthesis 12  Please note….. The three fatty acids of a triglyceride do not have to be identical They often differ markedly from one another 13  Triglyceride molecules non-polar Therefore, not soluble in water They clump together when placed in water 14 Note the clump formed 15  Saturated/Unsaturated fatty acids Saturated fatty acids = all bonds between C atoms in hydrocarbon chains are single bonds i.e. All bonds are saturated with H atoms Unsaturated fatty acids = hydrocarbon chains contain 1 or more double bonds 16  Animal triglycerides – usually long-chain saturated fatty acids tightly packed together. – are solid at room temperature Plant, vegetable, fish oils – usually short- chain unsaturated fatty acids, poorly pack together - are liquid at room temperature 17 18 19 20  Please note…. If a given fatty acid has more than one double bond: it is said to be polyunsaturated Double bonds prevent fat molecules from aligning closely with one another Hence they are liquid at room temperature (have low melting points) 21  Unsaturated Saturated No double bonds between carbon atoms; fatty acid chains fit close together Double bonds present between carbon atoms; fatty acid chains do not fit close together 22  Phospholipids Glycerol + 2 fatty acids + PO4 The phosphate has –ve electric charge= hydrophilic (“loves” water) Fatty acid tails = hydrophobic (“hates” water) Hydrophilic heads attracted to H2O Hydrophobic tails “hide” from H2O Phospholipids form cell membranes 23 24  At an oil-water interface, phospholipid molecules will orient so that their polar (hydrophilic) heads are in the polar medium, water, and their nonpolar (hydrophobic) tails are in the nonpolar medium 25 26  Steroids They are signal molecules Some are important part of the membranes Testosterone & estrogen: regulate sexual development in vertebrates 27  Cholesterol: Synthesized in the liver Part of structure in some membranes Starting material for making testosterone & other steroid hormones 28 Examples of steroids 29  From Cholesterol Sex Hormones What a big difference a few atoms can make! sex hormone is nearly always synonymous with sex steroid. 30  Nucleic Acids (DNA and RNA) Another class of Carbon-based molecules with unique properties Nucleic acids are polymers responsible for storage, transmission, and use of genetic information There are two types: - DNA (deoxyribonucleic acid) - RNA (ribonucleic acid) 31 31  Nucleic Acids (DNA and RNA) Composed of monomers called nucleotides consisting of: a pentose sugar (5 C) a phosphate-group (P with oxygen atoms) a nitrogen-containing base 32 32 Nucleotides vs Nucleosides Nucleotides consist of 3 components: a) Pentose sugar, b) Phosphate group, and c) Nitrogen-containing base. Nucleoside: comprises 2 items: a) Pentose sugar, and b) Nitrogenous base. Nucleic Acid Structures Reflect Their Functions RNA contains the sugar ribose. DNA contains the sugar deoxyribose. Nucleic Acid Structures Reflect Their Functions Nucleotides are linked by phosphodiester linkages. Phosphate groups link carbon 3′ in one sugar to carbon 5′ in another sugar. Nucleic acids grow in the 5′-to-3′ direction. Linking Nucleotides Together Linkages: A nucleotide consists of three components: a Nitrogen-containing base, a Pentose sugar (ribose in RNA), and one to three Phosphate groups Rest of polymer Phosphate Formation of the linkage Base between nucleotides The numbering of always occurs by adding ribose carbons is the the 5'-phosphate end of the basis for identification new nucleotide to the 3'-OH of 5' and 3' ends of end of the nucleic acid. DNA and RNA strands. Ribose 39 39  Differences between DNA and RNA DNA RNA The bases are: The bases are: Adenine Adenine Purines Purines Guanine Guanine Cytosine Cytosine Pyrimidines Prymidines Uracil Thymine The pentose sugar is The pentose sugar is Ribose. Deoxyribose. RNA is single stranded. DNA is double stranded. RNA does not have There is base-pairing in DNA. base-pairing. 40 RNA Molecule 3 end RNA (single-stranded) In RNA, the bases are attached to the ribose. The bases are Adenine (A) and Guanine (G) = [the purines]; and Cytosine (C) and Uracil (U) = the [pyrimidines]. 5 end DNA Molecule DNA (double-stranded) 5 end In DNA, the bases are 3 end attached to deoxyribose. Bases are: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T) (instead of uracil). DNA is double-stranded. Hydrogen bonds between purines and 3 end pyrimidines hold the two strands of DNA together. 5 end  In summary …chemical basis of life All elements are made up of unique atoms What makes different elements differ? There is finite # of known elements (see Periodic Table) Only some are essential for life - which ones? Elements make compounds through bonding of atoms The chemicals of “life” are the same in ALL living things See summary at end of Chapter 3 & 4 Next Origin of life 43 Q: Fats and Carbohydrates Fats rich in energy more than carbs Carbs used to provide energy to the cell Fats can provide energy when carbs are depleted 44 Why is starch digestible while cellulose is NOT?  Answer Both starches and cellulose are made of glucose molecules,..but the difference between them is that starch is a branched polymer, while cellulose is a linear polymer. This difference makes starch more digestible than cellulose.  Proteins Fibrous proteins covered in non-polar amino acids Do not dissolve into the aqueous solution Thank you Questions Comments 51  Lecture 14 The Chemical Basis of Life-5 ORGANIC MOLECULES: 2. Proteins Life Chap. 3 Describe the 4 levels of structure in a protein 1  Figure 3.3 Substances Found in Living Tissues Water (70%) 2  Lesson objectives Describe how amino acids differ in their side chains Describe how amino acids are joined to form a peptide Distinguish protein structures 3  Proteins Large, complex molecules Made up of many smaller units called amino acids, which are attached to one another in long chains. They are the basic building blocks of proteins Required for the structure, function, and regulation of the body’s tissues and organs. 4  Proteins have many roles Category Function Enzymes Catalyze biochemical reactions Structural proteins Provide physical stability & movement Signaling proteins Control physiological processes (e.g. hormones) Receptor proteins Receive & respond to chemical signals Membrane transporters Regulate passage of substances across cellular membranes Storage proteins Store amino acids for later use Transport proteins Bind & carry substances within the organism Gene regulatory proteins Determine the rate of expression of a gene 7 Keratin: structural protein of hair 8 ATP stores & transports energy in cells 9 Hemoglobin transports oxygen around the body 10 Carriers (membrane channels) 11  Protein Structure: Proteins are made up of one or more polypeptide molecules. Polypeptides are chains of amino acids  proteins can have 1 or more polypeptide chains folded & bonded together Have a complex 3-D shape 12 Polypeptides 13  Amino acids are the building blocks of proteins Proteins are polymers of 20 amino acids Arranged in a specific order 14 Amino acid structure 5 components  central carbon O H H  Hydrogen || |  amino group —C— C—OH —N—  carboxyl group (acid)  R group (side chain) |  variable group from 1 atom H R to 20.  confers unique chemical properties of the amino acid 15 Amino acid structure 16  Proteins are polymers of amino acids In addition to its R group, each amino acid,  when ionized, has a positive amino (NH3+) group at one end  and a negative carboxyl (COO–) group at the other end 17  The amino and carboxyl groups on a pair of amino acids can undergo a condensation reaction losing a molecule of water & forming a covalent bond A covalent bond that links two amino acids is called a peptide bond 18 19 20  More on building proteins Peptide bonds: dehydration synthesis linking NH2 of 1 amino acid to COOH of another C–N bond 21  More examples… Polypeptide chains N-terminal = NH2 end C-terminal = COOH end repeated sequence (N-C-C) is the polypeptide backbone grow in one direction Example: glycine & Phenylalanine 22  The two amino acids linked are not free to rotate around the N—C linkage…. because the peptide bond has a partial double-bond character…. unlike the N—C and C—C bonds to the central carbon of the amino acid 23  The stiffness of the peptide bond makes it possible for: chains of amino acids to form coils and other regular shapes 24 25  More on building proteins 2 amino acids linked to form a Dipeptide 3 amino acids linked to form a Tripeptide 4-10 amino acids linked by a peptide bond to form an Oligopeptide more than 10 amino acids linked to form a Polypeptide Proteins in the body and diet are long polypeptides (100s of amino acids) 26  Protein function depends on the shape of the molecule The shape of a protein determines its function 27 What Are the Chemical Structures of Proteins? The primary structure of a protein is its amino acid sequence. amino acid sequence is determined by DNA. slight change in amino acid sequence can affect protein’s structure & function. the sequence determines the secondary and tertiary structure i.e. how the protein is folded. Amino acid sequence 29  Levels of protein structure Primary structure  Specific amino acid sequence  determined by DNA  a protein can consist of any sequence of amino acids 30 31  Secondary structure Amino acid side groups are not the only parts of proteins that form hydrogen bonds The —COOH and —NH2 groups of the main chain also form hydrogen bonds 32  The polar groups of the main chain form hydrogen bonds with each other So what??? Two patterns of H bonding occur 33  In one pattern, hydrogen bonds form along a single chain,  linking one amino acid to another farther down the chain This tends to pull the chain into a coil called an alpha (α) helix 34 Note the hydrogen bonds!!! 35  In the other pattern: hydrogen bonds occur across two chains, Linking the amino acids in one chain to those in the other many parallel chains are linked forming a pleated, sheet like structure called a β-pleated sheet 36 A pleat sheet-like structure? 37 Note the hydrogen bonds!!! 38  The folding of the amino acid chain by hydrogen bonding into these characteristic coils.. and pleats is called a protein’s secondary structure 39 40  Tertiary structure The final folded shape of a globular protein Folds nonpolar side groups into the interior Protein is driven into its tertiary structure by hydrophobic interactions with water 41  The final folding of a protein is determined by its primary structure  By the nature of its side groups (hydrophobic/hydrophilic)  Many proteins can be fully unfolded (“denatured”)  and will spontaneously refold back into their characteristic shape 42 Folding determined by the nature of side groups 43  Quaternary structure Two or more polypeptide chains associating to form a functional protein  the individual chains are referred to as subunits of the protein  The subunits need not be the same  E.g. Hemoglobin is a protein composed of two α - chain subunits and two β-chain subunits 44  A protein’s subunit arrangement is called its quaternary structure 45  In summary: Protein Structure… Primary Assembly STRUCTURE PROCESS Secondary Folding Tertiary Packing Quaternary Interaction 46  Thank you.. Questions Comments 47 The Chemical Basis of Life-4 ORGANIC MOLECULES: 1. Carbohydrates Dr G. Tsheboeng 235/231 1 Recap: Making Biological Molecules and H2O Condensation Reaction 2 substances combine = form one new compound plus water H2O Hydrolysis Reaction Water is “added” to one compound = it breaks into 2 bits 2  E.g. Hydrolysis reaction 6CO2 + 6H2O + Energy -> C6H12O6 + 6O2 (photosynthesis) Condensation reaction C6H12O6 + 6O2 -> 6CO2 + 6 H2O+ Energy (686 kcal). (respiration) 3  Lesson objectives To define organic molecules To list examples of functional groups To discuss the synthesis of organic molecules To discuss the different types of carbohydrates 4  Organic molecules What is an organic molecule? A molecule that is normally found in or produced by living systems.. Typically consists of carbon atoms in rings or long chains,  where other atoms (e.g. hydrogen, oxygen, and nitrogen) are attached. 5  Molecules are the building blocks of life The chemistry of carbon: o Biological molecules consist mainly of carbon atoms o Bonded to other carbon atoms o Or to atoms of O, S, N or H o Can form 4 covalent bonds o Carbon molecules can form straight chains, branches or rings 6 These generate a lot of molecular structures & shapes 7  Hydrocarbons Only contain carbon & hydrogen Covalent between carbon & hydrogen energy rich Because of these they make good fuels 8 Examples of hydrocarbons 9 Gasoline used for fuel in cars is also rich in energy 10  Functional groups Due to similar electro-negativities, C-C & C-H hydrocarbon molecules are non-polar However, most organic molecules contain other atoms These atoms often have different electro- negativities Hence they are polar 11  Remember: Electronegativities of elements important to life Element Electronegativity Oxygen 3.5 Chlorine 3.1 Nitrogen 3.0 Carbon 2.5 Phosphorous 2.1 Hydrogen 2.1 Sodium 0.9 Potassium 0.8 12  Specific groups attached to C-H molecules are called functional groups E.g. –OH (hydroxyl group) Functional groups maintain their chemical properties Biological chemical reactions involve functional groups 13 More examples of functional groups 14  Building Biological Molecules and H2O Condensation/dehydration Reaction 2 substances combine = form one new compound plus water H2O Hydrolysis Reaction Water is “added” to one compound = it breaks into 2 bits 15  Remember… Hydrolysis reaction 6CO2 + 6H2O + Energy -> C6H12O6 + 6O2 (photosynthesis) Condensation reaction C6H12O6 + 6O2 -> 6CO2 + 6 H2O+ Energy (686 kcal). (respiration) 16 Making Biological Molecules Condensation Hydrolysis 17  Condensation reaction Called dehydration synthesis because – OH group & H are removed H2O removed Energy is required to break the chemical bonds as water is removed Cell must supply energy to build macromolecules 18  Hydrolysis Reverse of dehydration Molecule of water is added Release the energy that was stored in the bonds 19  Four main categories of Organic molecules Carbohydrates Proteins Lipids and Nucleic acids ( DNA and RNA) 20  Carbohydrates Carbohydrates are the main energy source for living things The name "carbohydrate" means a "hydrate of carbon.“ Chemically, carbohydrates are organic molecules in which carbon, hydrogen, and oxygen bond together in the ratio: Cx(H2O)y where x and y are whole numbers that differ depending on the specific carbohydrate 21 Carbohydrates are made from simple sugars 22 Carbohydrates Make up a large group of molecules o Have similar atomic compositions o Differ in size, chemical properties & biological functions 23  Carbohydrates have four major biological roles They are used as a source of stored energy They are used to transport stored energy within complex organisms They serve as carbon skeletons that can be rearranged to form new molecules They form extracellular assemblies such as cell walls that provide structure to organisms 24  Monosaccharides are simple sugars All living things contain the monosaccharide glucose o It is the “blood sugar” o Used to store & transport energy in in humans o Exists in straight chains and ring forms o Ring forms dominant because they are stable in water 25  Four categories of biologically important Carbohydrates All carbohydrates are made up of units of sugar (also called saccharide units). Simple sugars = carbohydrates that contain a single sugar unit = monosaccharides (Monomers) or Two sugar units = disaccharides (Dimers) Three-twenty= Oligosaccharides (oligo, “several”) Many sugar units (>2) = polysaccharides (Polymers) 26  Types of sugars An aldose is a monosaccharide (a simple sugar) that contains only one aldehyde (-CH=O) group per molecule. A ketose is a sugar containing one ketone (-C=O) group per molecule 27 Examples of ketoses and aldoses 28  Different Monosaccharides contain different numbers of carbons The building blocks of all higher carbohydrates. All have a general molecular formula (CH2O)n. further classified, based on the number of carbon atoms in a molecule Trioses - contain 3 carbon atoms: glyceraldehyde Tetroses - contain 4 carbon atoms: malate Pentoses - contain 5 carbon atoms: ribose, deoxyribose, ribulose hexoses - contain 6 carbon atoms: glucose, fructose, galactose 29  Some monosaccharides are structural Isomers Are compounds with the same O H O H molecular formula but different structural formulas. C C Isomers have different H – C – OH HO – C – H arrangements of atoms. HO – C – H H – C – OH H – C – OH HO – C – H H – C – OH HO – C – H CH2OH CH2OH D-glucose L-glucose 30  D-Glucose: Three hydroxyl groups & one hydrogen group are on the right side L-Glucose: They are on the left 31 Three Monosaccharides C6H12O6 32 Structural differences between Glucose, Galactose & Fructose 33 34 35  Glycosidic bonds link monosaccharides Disaccharides Made up of combination of 2 monosaccharides Could be the same or different types of monosaccharides Sucrose, common “table sugar”, consists of a glucose unit bonded to a fructose unit The 2 monosaccharides form covalent bonds The covalent bonds are called glycosidic bonds The bonding results in loss of an H2O molecule 36  Formation of Disaccharides Same monomers Different monomers NB: dehydration 37 Common table sugar- Different monomers 38 Breaking up: hydrolysis NB: Digestion of sucrose 39  Transport disaccharides Most organisms transport glucose in their bodies In humans it is transported as monosaccharide In plants & other organisms it is converted in transport form 40  In transport form is less readily metabolized Transported in disaccharide form Disaccharide is effective glucose reservoir Glucose utilizing enzymes cannot use it Enzymes that can break are only found in the tissues where it should be used 41  E.g. of transport disaccharides Sucrose (Glucose + Fructose) in plants Glucose + Galactose= Lactose in mammals Adults have reduced levels of lactase Therefore cannot use lactose efficiently 42  Polysaccharides…. Consist of several hundred monosaccharide units forming giant chains of monosaccharides joined by glycosidic bonds Polysaccharides are not soluble in water The monosaccharide units may be of the same type or different types If same type = homopolysaccharide Starch & cellulose = made up of glucose only If different types = heteropolysaccharide 43  Polysaccharides store energy & provide structural materials 44 Important Polysaccharides: Storage: starch & glycogen Consists of glucose Glycogen: subunits shorter chains Product of photosynthesis Plant energy storage molecule Glycogen is a similar molecule in animals. Starch and glycogen can be digested by animals. 45 Important Polysaccharides: Structural: Cellulose Composed of glucose subunits Different bond from starch formed Structural component in plants cell walls Cannot be digested by animals 46 Important Polysaccharides: Structural: Chitin Glucose subunits Partly derived from non-sugars (nitrogen) Composes exoskeletons of insects Water proof Note similarity to cellulose. 47 48  Summary Questions Comments 49