Biomolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids PDF

6/4/22 4 Carbon Based Biomolecules Compose Cells The Nature of Science Cellulose is a carbohydrate made up of sugar molecules Biomolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids 1306: Intro Bio for Majors Jenifer Gifford, Ph.D. [email protected] Cellular membranes are composed of lipid...

6/4/22 4 Carbon Based Biomolecules Compose Cells The Nature of Science Cellulose is a carbohydrate made up of sugar molecules Biomolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids 1306: Intro Bio for Majors Jenifer Gifford, Ph.D. [email protected] Cellular membranes are composed of lipids and proteins The nucleus houses Chromosomes, which are composed of the nucleic acid, DNA Recall: Monomers Together to Form Polymers The Join Nature of Science Monomers are the building blocks of polymers, which are macromolecules Biomolecule Monomer Polymer Carbohydrates Monosaccharides (sugar) Polysaccharides Proteins Amino Acids Polypeptides Nucleic Acids Nucleotide Nucleic Acid (DNA/RNA) Learning Goals For Each of the 4 Biomolecules (Proteins, Fats, Carbs, and Nucleic Acids): • Know which monomers form each polymer (ex. amino acids form polypeptide proteins) • Be able to identify each monomer and polymer by it’s structure • Describe the variety of structures within each class of biomolecules • Describe and understand how saturation affects lipid structure and function • Understand the terms of primary, secondary, and tertiary structure in the context of Nucleic Acids and Proteins. • Provide functional examples of each biomolecule in cells Lipids/Fats are weird and don’t follow this pattern 1 6/4/22 Section Break: Lipids The Nature of Science • Are an integral part of cellular membranes, • • • • General Terminology The Nature of Science Lipids: Catch-all term for carbon containing compounds that are insoluble in water • Insolubility due to a high proportion of nonpolar and C—H bonds • Lipids can dissolve, but only in nonpolar solvents like benzene (“like dissolves like”). Hydrocarbons- nonpolar molecules that contain only carbon and hydrogen • Hydrophobic • Electrons are shared equally in C—H bonds, which does not generate partial charges • Therefore, lipids are insoluble because they have a large hydrocarbon component. which separates life from non-life Are a source of long term energy for cells Act as pigments to capture/respond to sunlight Form waterproof coverings Vitamin transport and absorption 4 Types The NatureofofLipids Science Triglycerides are our Dietary Fats The Nature of Science • Triglycerides are composed of a glycerol attached to fatty acid tails • The primary role of triglyceride fats is energy storage: • Large number of high-energy bonds in fatty acid chains • Bonds allow fats to store twice as much chemical energy 2 6/4/22 How does The “saturation” properties? Nature ofaffect Science Saturation changes physical state: • Foods that contain lipids with double bonds said to be healthier Steroids form theThe basis for Cholesterol Nature of Science and Hormones Steroids are distinguished by bulky, four-ring structure and differ from one another by functional groups attached to carbons in rings Examples: • Hormones estrogen and testosterone • Cholesterol, component of plasma membranes Fluidity Fluidity • Unsaturated Lipids • Highly unsaturated lipids are liquid at room temperature and above Saturated Fat Temperature • Saturated lipids: • Highly saturated lipids are solid at room temperature • Saturated lipids with long hydrocarbon tails are stiff solids at room temperature Temperature Fatty Acid TailsThe canNature Be Saturated or Unsaturated of Science Fatty acid—hydrocarbon chain bonded to a carboxyl (–COOH) functional group: • Can be saturated or unsaturated • Saturated—hydrocarbon chains consist of only single bonds between carbons • Unsaturated hydrocarbon chains have one or more double bonds in hydrocarbon chains: • Hydrogen atoms are removed to make double bond • Forms “kink” in chain • Polyunsaturated chains have many double bonds Phospholipids Form Cellular Membranes The Nature of Science Phospholipids: • Primary role of phospholipids is to form cell membranes • Consist of glycerol linked to a phosphate group and hydrocarbon chains • The identity of the hydrocarbon chains can tell you what kind of organism the lipid is from: • fatty acid tails—found in domain Bacteria and Eukarya • isoprenoid tails—found in domain Archaea A) Cholesterol 3 6/4/22 The Nature Science Phospholipids areofAmphipathic Phospholipids are amphipathic: • Substances with both hydrophilic and hydrophobic regions • Hydrophilic “head” region contains: • Glycerol • Negatively charged phosphate group • Charged or polar group • Hydrophobic Hydrocarbon “tail” contains • String of C-H bonds • Phospholipids can have one or two tails • Tails can be saturated or unsaturated • Water molecules cannot form hydrogen bonds with tail The Nature Science How Phospholipids Behaveofand Interact In Water Water Liposomes Water Nature ofof Science SelectiveThe Permeability Lipid Bilayers • Phospholipid bilayers have selective permeability: • Small or nonpolar molecules move across phospholipid bilayers quickly • Charged or large polar substances cross slowly, if at all • Examples: • Oxygen: Small nonpolar molecule moves quickly across bilayers • Glucose: Large polar molecule moves slower across bilayer • Sodium ions (Na+) do not move through unaided • Amphipathic lipids do not dissolve in water. Instead, hydrophilic heads interact with water and hydrophobic tails do not • In water, amphipathic lipid molecules associate and form: • Micelles: Tiny spherical aggregates • Lipid bilayers: Created when lipid molecules align in paired sheets • Each can form spontaneously • Lab created membranes (liposomes and planar bilayers) are used to study permeability Degree of Saturation and Length Affects Fluidity and The Nature of Science Permeability Unsaturated Not all phospholipids are the same. Length and Saturation of hydrocarbon tails and the presence of cholesterol molecules can influence the permeability of a bilayer Saturated • Unsaturated= Higher Permeability • Double bonds in hydrocarbon tails can cause “kinks” in hydrocarbon chain that pushes hydrophobic tails apart. This weakens barrier to solutes and allows more movement within the membrane • Saturated = Lower Permeability • Hydrocarbon tails with single bonds have fewer spaces and stronger hydrophobic interactions. This makes membrane dense and tightly packed, limiting movement and permeability • Length of Tails: Hydrophobic interactions become stronger as saturated hydrocarbon tails increase in length, which also decreases permeability. 4 6/4/22 Lipids Summary The Nature of Science • Lipids: • Have wide array of functions: • Store chemical energy, Act as pigments that capture/respond to sunlight, Serve as signals between cells, Form waterproof coatings on skin and cells, Act as vitamins in cellular processes, Forms the cellular membrane • Are composed of hydrogen and carbon atoms that form hydrocarbon chains. These chains can be saturated or unsaturated • Is a term that includes 4 major types of molecules: Steroids, fats, phospholipids, and waxes • Phospholipids are amphipathic and are responsible for making the cellular membrane. • The cellular membrane is fluid and selectively permeable • Lipid structure, %composition, and temperature can change the fluidity and permeability of a membrane Carbohydrate The Nature ofStructure Science • Carbohydrates are composed of monomers called saccharides • Single saccharides (monosaccharides) bond together to make oligosaccharides/ disaccharides and polysaccharides. The Nature of Science Section Break: Carbohydrates • Are composed of monosaccharide sugar molecules that join together to make polysaccharides • Serve as building blocks for larger molecules • Provide short term chemical energy in cells • Provides structural integrity for structures such as cell walls The Nature of Science Carbohydrate Monomeric Structure • Carbohydrates have the molecular formula (CH2O)n • N= the number of carbon hydrate groups/units • N can vary from 3, in the smallest sugars to over a thousand • Carbohydrates contain carbonyl groups (C=O), hydroxyl groups (-OH) and multiple C-H bonds • But not all CHO compounds are considered carbohydrates 5 6/4/22 Variety in Monomeric Carbohydrate The Nature of Science Structure Many distinct monosaccharides exist because so many aspects of their structure are variable: • Aldose or ketose placement of the carbonyl group • Variation in carbon number (triose vs. hexose) • Different arrangements of hydroxyl groups in space • Alternative ring forms Polysaccharide The Nature ofStructure Science • • • What are the carbohydrates? Thefunctions Nature ofofScience Structural Support The Nature of Diverse Science Functionality Structural Diversity leads to 1. Serves as precursors molecules to • other molecules, such as nucleotides and amino acids 2. Can provide fibrous structural materials • 3. Indicate cell identity 4. Energy Storage Polysaccharides, or complex carbohydrates, are polymers of monosaccharide monomers Two sugars linked together form a disaccharide Sugars are linked when a condensation reaction occurs between two hydroxyl groups which forms a covalent bond called a glycosidic linkage • Cellulose, chitin, and peptidoglycan are 3 distinct carbohydrates that form long strands with bonds between adjacent strands: • Strands may be organized into fibers or sheets • Gives cells and organisms strength and elasticity These particular glycosidic linkages are not easy to hydrolyze: • Most organisms lack enzymes to hydrolyze them • These fibers exclude water, making hydrolysis difficult Carbohydrates form dietary fiber—important for digestive health 6 6/4/22 What are the carbohydrates? Thefunctions Nature ofofScience Energy Storage What are the carbohydrates? Thefunctions Nature ofofScience Energy Storage • Energy can be transferred during chemical reactions (making and breaking • Carbohydrates store and provide chemical energy within their bonds chemical bonds) • In photosynthesis, plants harvest energy from sunlight and store it in the bonds of carbohydrates, which are broken during cellular respiration • During cellular respiration the bonds in sugar are broken during chemical • Carbohydrates store more energy than CO2 • Electrons in C=O and C—O bonds are held tightly and have low potential energy. reactions to make ATP, which is the energy rich molecules that does work within a cell (such as powering the cellular machinery responsible for muscle contraction • Electrons in C—H and C—C bonds are weaker and have high potential energy What are the carbohydrates? Thefunctions Nature ofofScience Energy Storage Plants store sugars as starch • Composed of a-glucose monomers • Forms a helix • Starches can be long chains with branched structures • Amylose and Amylopectin are both starches with differences in their structures Animals store sugar as glycogen • Highly branched α-glucose polymer, nearly identical to starch: • Branches occur in about 1 out of 10 monomers • Stored in liver and muscle cells • Can be broken into glucose monomers for energy What are the carbohydrates? Thefunctions Nature ofofScience Cell Identity • Carbohydrates indicate cell identity • Display information on the outer surface of cells: • Glycoproteins—proteins with attached carbohydrates • Glycolipids—lipids with attached carbohydrates • Glycoproteins and glycolipids are key molecules in: • Cell–cell recognition: Identify cells as “self” • Cell–cell signaling: Communication between cells 7 6/4/22 The Nature ofSummary Science Carbohydrates Carbohydrates: • are molecules composed of different arrangements of Carbon, hydrogen, and oxygen. • Are a polymer composed of monosaccharides • are important for energy storage, determining cell identity, and providing structural support. • Have diverse structural arrangements, which results in diverse carbohydrate based structures like cellulose, chitin, and peptidoglycan The Nature of Science Section Break: Proteins Proteins: • Are composed of amino acids that join together to form 4 major levels of structure • Perform many of the functions within a cell including enzyme catalysis, membrane transport, and cellular signaling and are responsible for the phenotypes we can observe The Nature ofwith Science Protein Structure Starts Amino Acids Amino acids are composed of a central carbon atom bonded to: 1. H—hydrogen atom 2. NH2—amino group 3. COOH—carboxyl group 4. R group—variable “side chain” In water, amino and carboxyl groups ionize to N H3+ and COO− respectfully • Charges on functional groups necessary because they help amino acids stay in solution and affect amino acid’s chemical reactivity Protein Structure: The Nature of Science Amino Acid Side Chains • R-group, or side chain, represents the part of an amino acid core structure that makes each of 20 amino acids unique • Properties (such as solubility and reactivity) of amino acids vary because R-groups vary – Charged, uncharged polar, and nonpolar – Polar and charged R-groups interact with water—are hydrophilic – Nonpolar R-groups are hydrophobic— do not form hydrogen bonds with water • Some side chains contain functional groups that can participate in chemical reactions. Others have no functional groups and solely consist of carbon and hydrogen atoms 8 6/4/22 TypesThe of Amino Side Chains NatureAcid of Science 1. 2. 3. 4. Does side chain have negative charge? If so, it lost a proton to the solution and is acidic. Does side chain have a positive charge? If so, it gained a proton from the solution and is basic If side chain is uncharged, does it have an oxygen atom? Highly electronegative oxygen will form polar covalent bond, uncharged polar Did you say no to the last three questions? Then it’s a plain ol’ nonpolar side chain Complete Polypeptide The Nature of Science Oligopeptide (“few-peptides”) or peptide: Chain of fewer than 50 amino acids Polypeptide (“many-peptides”):Chain of more than 50 amino acids Protein: describes the full chain of amino acid residues. It is the complete, functional form of molecule The Nature of Science Protein Structure: Amino Acid Side Chains • Proteins are a polymer that is formed by the joining of amino acids • Amino acids polymerize when bond forms between carboxyl group of one amino acid and an amino group of another • Peptide Bonds, C—N, are covalent bonds that form during a condensation reaction. • Proteins fold, but the peptide bond itself cannot rotate. The single bonds on either side can rotate instead. The Nature Science What do proteins in theiroffinal form look like? Structure gives rise to function: • Proteins have unparalleled diversity of size, shape, and chemical properties of amino acid residues • Proteins serve diverse functions in cells because structure gives rise to function 9 6/4/22 4 Levels The of Protein NatureStructure: of SciencePrimary • Primary structure: – Each protein has unique sequence of amino acids – Number of primary structures practically limitless as there are 20 types of amino acids available to create over 10,000 billion variations – Lengths range from two amino acid residues to tens of thousands – Amino acids are connected by covalent bonds 4 Levels of Protein TheStructure: Nature of Science Secondary NatureStructure: of SciencePrimary 4 Levels The of Protein Modifying the primary structure can have a dramatic effect on the final structure and functionality. Example: Hemoglobin: Change in R-group produces hemoglobin molecules that stick to one another NatureStructure: of ScienceTertiary 4 Levels The of Protein • Protein secondary structure formed by hydrogen bonds between: – Carbonyl group of one amino acid – Amino group of another amino acid • Types of secondary structures: • α-helix (alpha-helix) • β-pleated sheet (beta-pleated sheets) • Protein’s tertiary structure: – Results from interactions between residues (next slide) – These interactions cause backbone to bend and fold • Bending and folding contribute to distinctive three-dimensional shape of polypeptide 10 6/4/22 4 Levels The of Protein NatureStructure: of ScienceTertiary 4 Levels of Protein Structure: The Nature of Science Tertiary Structure and Mutations Five important types of R-group interactions: 1. Hydrogen bonding—form between polar side chains and opposite partial charges 2. Hydrophobic interactions—water forces hydrophobic side chains together 3. van der Waals interactions—weak electrical interactions between hydrophobic side chains 4. Covalent bonding—covalent bonds between side chains of sulfhydryl groups (disulfide bonds) 5. Ionic bonding—form between groups with full and opposing charges Nature of Science 4 Levels ofThe Protein Structure: Quaternary 45 The NatureHierarchy of Science Structure Quaternary structure – Is the result of multiple fully folded polypeptide chains (a subunit) binding together to make a larger molecular machine – Creates dimers, trimers, and larger multi-protein complexes – Example: Hemoglobin contains 4 subunits. 2 alpha/2 beta – Ribosomes consist of 50 different polypeptides and several nucleic acid molecules 47 11 6/4/22 Protein Folding: TheStructure Nature ofDetermines Science Function • Normal protein folding is crucial and often spontaneous: – Result of chemical bonds and interactions – Folded molecule more energetically stable than unfolded molecule— less potential energy • Denatured (unfolded) protein unable to function normally TheEnzymes Nature of Science Protein Functions: and Chemical Reactions • Catalyzed reactions involve reactants called substrates • Enzymes: – Proteins that function as catalysts – Hold substrates in precise orientation: • Makes a reaction more likely to occur – Have active site—location on an enzyme where substrates bind and react The do?.... NaturePretty of Science What do proteins much everything • Proteins are crucial to most tasks required by cells: – Catalysis—speed up chemical reactions (next slide) – Structure—shape cells and comprise body structures – Movement—motor proteins move cells or molecules within cells – Signaling—convey signals between cells – Transport—allow molecules to enter and exit cells or carry them throughout the body – Defense—antibodies attack pathogens The Nature of Science Section Break: Nucleic Acids • Are composed of nucleotides (ATCG) that join together to form 3 major levels of structure • Two major types: DNA and RNA • Carry the information necessary to produce proteins within a cell 12 6/4/22 TheStructure Nature ofPrimary ScienceStructure Nucleic Acid Nucleic acid—polymer of nucleotide monomers Three pieces of nucleotide: 1. Phosphate group 2. Five-carbon sugar 3. Nitrogenous (nitrogencontaining) base Phosphate group and nitrogenous base are bonded to sugar molecule The Nature Science Base Nucleic Acid PrimaryofStructure: Two groups of nitrogenous bases: 1. Purines—contain nine atoms in their two rings: • Adenine (A) • Guanine (G) The Nature Science Sugar Nucleic Acid PrimaryofStructure: • Ribonucleotides are monomers of RNA: • Have ribose as their sugar • Has an –OH group bonded to the 2’ carbon • Deoxyribonucleotides are the monomers of DNA: • Sugar is deoxyribose (deoxy = “lacking oxygen”) • Has H instead at 2ʹ carbon • Both sugars have an –OH group bonded to the 3’ Carbon Nucleotides Come Together The Nature of Science to Form the Primary Structure of Nucleic Acids 5 • Nucleic acids polymerize via condensation reactions • Phosphodiester linkage (bond) occurs between: • Phosphate group on 5ʹ carbon of one nucleotide and the –OH on the 3’ carbon on the other 2. Pyrimidines—contain six atoms in their one ring: • Cytosine (C) • Uracil (U)—found only in ribonucleotides • Thymine (T)—found only in deoxyribonucleotides • Think of it as “C U T of P y” 3 13 6/4/22 Nucleotides Come Together The Nature of Science to Form the Primary Structure of Nucleic Acids Sugar Phosphate Backbone is Formed Nucleotides Come Together The Nature of Science to Form the Primary Structure of Nucleic Acids • Backbone is directional (5ʹ → 3ʹ direction): • One end has unlinked 5ʹ phosphate group • Other end has unlinked 3ʹ hydroxyl group • Primary structure of D N A written by listing sequence of bases by single-letter abbreviations: • Example: 5’-TGCA-3’ DNA TheSecondary Nature ofStructure: Science Complimentary Base Pairing DNA is an anti-parallel double stranded helix with complimentary base pairs DNA TheSecondary Nature ofStructure: Science Antiparallel Strands Antiparallel Strands Chargaff analyzed the DNA base compositions across species and demonstrated variations in DNA from species to species. 1) DNA base composition varies between species. 2) % of A’s and T’s are equal and % of C’s and G’s are equal 14 6/4/22 RNA Structure and Function Primary structure of RNA: • Four types of nitrogenous bases extending from sugar–phosphate backbone Primary structure of RNA differs from DNA: 1. RNA contains ribose instead of deoxyribose 2. RNA contains uracil instead of thymine 3. RNA much less stable than DNA RNA Structure • RNA molecules can also have tertiary structure: • Forms when secondary structures fold into more complex shapes • RNA much more diverse in size, shape, and reactivity than DNA RNA Structure and Function • RNA’s secondary structure results from complementary base pairing: A with U; G with C • RNA strand folds over, forming hairpin structure: – Bases on one part of RNA strand fold over and align with bases on other part of the same strand – Hydrogen bonding associates complementary bases RNA Function RNA highly versatile: – Folds into complex threedimensional shapes – Structure flexibility allows them to perform many tasks – As intermediate between DNA and protein, mRNA transmits information to produce proteins – Ribozymes are capable of catalyzing reactions like proteins – Can regulate production of mRNA from DNA 15 6/4/22 DNA vs. RNA Structure 16