* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download c - SchoolRack
Citric acid cycle wikipedia , lookup
Two-hybrid screening wikipedia , lookup
Size-exclusion chromatography wikipedia , lookup
Photosynthesis wikipedia , lookup
Point mutation wikipedia , lookup
Isotopic labeling wikipedia , lookup
Peptide synthesis wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Fatty acid synthesis wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Genetic code wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Protein structure prediction wikipedia , lookup
Fatty acid metabolism wikipedia , lookup
Metalloprotein wikipedia , lookup
Proteolysis wikipedia , lookup
AP & Adv. Biology Honors • Needed for Class: – 3-Ring Binder (D-Rings are best): You might start with a 2.5” or a 3.0” binder. At midterm, you will probably need a second binder of similar size. – Dividers for Binder, labeled • • • • – – – – Daily Journal Class Notes Homework/Classwork, Study Guides, Labs Tests/Quizzes Pens/Pencils Colored Pencils Kept in Binder Highlighter White Board Markers (optional) 1 Other Items • Logistics: – Come to class ON TIME – Upon arrival, turn to Daily Journal and answer the day’s question appropriately. Do not skip any questions. – Remove all items from your desk except binder – No food, snacks, etc. – No cell phones out, in lab, etc. – Keep binder neat and sectioned – Focus: i.e., “Let the dude in the front do your studying” • Think of YOUR FUTURE. You want to What?__________________ • Think College • How will you succeed there if 90+% of your grade comes from 3-4 Tests? • If college classes don’t collect homework, then what is the purpose of homework/classwork, etc? • If there are only 3 tests/Semester, and 12 Chapters are covered per semester, then each test will cover how many chapters?______ • How will you learn that volume of material for the “long-term?” 2 Other Items • Grading – Tests = 75% • Are Cumulative • Later tests in a Term count more than initial tests in the same term, with each term ending with a “Term Exam” • When will you do your studying for each test? • How will you remember the material a year from now (Think College)? – Labs, Study Guides, Homework, Classwork, Binder = 25% • Are not all equal. Some labs are more complex than others, and count more. Same for all other work. • Due dates will be clear, and often, work is due on the day of the exam. • Study Groups? • AP vs. Honors Levels – AP receives extra readings, extra study guide questions, extra essay and MC questions on tests, etc. – Honors receives a grade “boost” • Extra Lab Time/Extra Help Times – Will be Posted a week in advance. – Get a pass the day before you plan to come in 3 Chapter 2: Basic Chemistry Highlites Essential Elements of Life About 25 of the 92 elements are essential to life Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are those required by an organism in minute quantities CHNOPS 5/23/2017 4 Isotopes • Atoms of an element have the same number of protons but may differ in number of neutrons • Isotopes are two atoms of an element that differ in number of neutrons • Most isotopes are stable, but some are radioactive, giving off particles and energy • Some applications of radioactive isotopes in biological research: – Dating fossils – Tracing atoms through metabolic processes – Diagnosing medical disorders 5/23/2017 5 LE 2-7b Third energy level (shell) Second energy level (shell) Energy absorbed First energy level (shell) Energy lost Atomic nucleus 5/23/2017 6 LE 2-12 – O H + 5/23/2017 H H2O + 7 Chapter 3: Water and the Fitness of the Environment – Water is the biological medium here on Earth – All living organisms require water more than any other substance • Three-quarters of the Earth’s surface is submerged in water • The abundance of water is the main reason the Earth is habitable Figure 3.1 • Concept 3.1: The polarity of water molecules results in hydrogen bonding • The water molecule is a polar molecule • The polarity of water molecules – Allows them to form hydrogen bonds with each other – Contributes to the various properties water exhibits – Hydrogen bonds + H + Figure 3.2 – – + H + – Qualities of Water that are caused by its polarity and the biological significance of those qualities • Water molecules exhibit cohesion: Water attracts to water as it hydrogen bonds to itself • Biological Significance: Qualities of Water that are caused by its polarity and the biological significance of those qualities • Water has a high specific heat: • Biological Significance – Moderate Temperature – High Heat of Vaporization – Ice Floats Qualities of Water that are caused by its polarity and the biological significance of those qualities Water is a versatile Solvent • Biological Significance – Reactions within and outside cells – Rings of Hydration – Interacts with Polar Molecules, such as some proteins – Hydrophilic Materials – Hydrophobic Materials Qualities of Water that are caused by its polarity and the biological significance of those qualities • Dissociation of water molecules leads to acidic and basic conditions that affect living organisms • Water can dissociate into hydronium ions (H3O)+ and hydroxide ions (OH-) • Changes in the concentration of these ions can have a great affect on living organisms – + H H H H Figure on p. 53 of water dissociating H H H Hydronium ion (H3O+) Results in free H+ ions + H Hydroxide ion (OH–) Qualities of Water that are caused by its polarity and the biological significance of those qualities • Acids: • Bases: • The pH Scale • Biological Significance of Acids and Bases – Transport of hormones in plants – Alteration of protein structures for • Activation • Denaturing • If acids and bases are potentially harmful to cells and living things, what prevents harm? Why can a person drink a quart of orange juice without sustaining a lethal change in blood pH? – The Answer – Applications • Swansea Dam • Lungs and Small Intestine Chapter 4 Carbon and the Molecular Diversity of Life • • Overview: Carbon—The Backbone of Biological Molecules All living organisms – Are made up of chemicals based mostly on the element carbon • Concept 4.1: Organic chemistry is the study of carbon compounds • Organic compounds – Range from simple molecules to colossal ones Figure 4.1 • The concept of vitalism – Is the idea that organic compounds arise only within living organisms – Was disproved when chemists synthesized the compounds in the laboratory EXPERIMENT RESULTS In 1953, Stanley Miller simulated what were thought to be environmental conditions on the lifeless, primordial Earth. As shown in this recreation, Miller used electrical discharges (simulated lightning) to trigger reactions in a primitive “atmosphere” of H2O, H2, NH3 (ammonia), and CH4 (methane)— some of the gases released by volcanoes. A variety of organic compounds that play key roles in living cells were synthesized in Miller’s apparatus. Organic compounds may have been synthesized abiotically on the CONCLUSION early Earth, setting the stage for the origin of life. (We will explore Figure 4.2 this hypothesis in more detail in Chapter 26.) • Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms • Carbon has four valence electrons • This allows it to form four covalent bonds with a variety of atoms • The bonding versatility of carbon – Allows it to form many diverse molecules, including carbon skeletons Name and Comments Molecular Structural Formula Formula H (a) Methane CH4 H C H H (b) Ethane H H C2H H C C H 6 (c) Ethene Figure 4.3 A-C (ethylene) H H H C2H4 H C C H H Ball-andStick Model SpaceFilling Model • The electron configuration of carbon – Gives it covalent compatibility with many different elements: i.e., it can bond covalently with many other kinds of atoms. Figure 4.4 Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C Molecular Diversity Arising from Carbon Skeleton Variation • Carbon chains – Form the skeletons of most organic molecules – Vary in length and shape H H H H C C C H H H H Propane H H C H H H H H H H (b) Branching H C C C C H H C C C H H H H H H H H 2-methylpropane Butane (commonly called isobutane) H H H H H H H H (c) Double bonds H H C C C C H C C C C H H H H H 1-Butene 2-Butene H H H H C H H C C H C H (d) Rings H C C H H C C H H C C C (a) Length Figure 4.5 A-D H H H C C H H H Ethane Cyclohexane Benzene Hydrocarbons • Hydrocarbons Are molecules consisting of only carbon and hydrogen – Are found as parts of many of life’s vital organic molecules Fat droplets (stained red) Figure 4.6 A, B (a) A fat molecule 100 µm (b) Mammalian adipose cells Concept 4.3: Functional groups are the parts of molecules involved in chemical reactions – Are the chemically reactive groups of atoms within an organic molecule – Give organic molecules distinct properties. Estradiol OH CH3 HO Female lion OH CH3 CH3 O Figure 4.9 Male lion Testosterone • Some important functional groups of organic compounds FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O OH (may be written HO C C OH ) STRUCTURE In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) Figure 4.10 O The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is doublebonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (— COOH). • Some important functional groups of organic compounds NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) EXAMPLE H H H C C H H Ketones if the carbonyl group is Carboxylic acids, or organic within a carbon skeleton acids Aldehydes if the carbonyl group is at the end of the carbon skeleton H OH H C H C H H Ethanol, the alcohol present in alcoholic beverages H O C H C OH H H Acetone, the simplest ketone H Figure 4.10 C O H H C C H H O C Propanal, an aldehyde H Acetic acid, which gives vinegar its sour tatste • Some important functional groups of organic compounds AMINO SULFHYDRYL H N H Figure 4.10 O SH (may be written HS The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. PHOSPHATE ) O P OH OH The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (— OPO3H2; note the two hydrogens). • Some important functional groups of organic compounds H O C HO C H H N H H Glycine Figure 4.10 H H C C H H OH OH H SH H C C C H H H O O P O O Ethanethiol Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Glycerol phosphate Chapter 5 The Structure and Function of Macromolecules • Macromolecules – Are large molecules composed of smaller molecules (polymers) – Are complex in their structures Concept 5.1: Most macromolecules are polymers, built by joining identical or similar monomers into long chains. Three of the classes of life’s organic molecules are polymers – Carbohydrates: Sugars, Starch Figure 5.1 – Proteins – Nucleic acids: DNA, RNA The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration reactions HO 1 3 2 H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO Figure 5.2A 1 2 H HO 3 H2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer • Polymers can disassemble by – Hydrolysis HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H Figure 5.2B (b) Hydrolysis of a polymer H H2O HO H Sugars Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers Triose sugars Pentose sugars (C3H6O3) (C5H10O5) H O H Aldoses C O H H O C C OH H C OH H C OH H C OH H C OH HO C H C OH H H C OH H H H H C H C OH H HO C H C OH HO C H H C OH H C OH H C OH H C OH H H Glucose Galactose H C OH H C O H C OH H C OH C O O C OH H C OH HO H H C OH H C OH Dihydroxyacetone H C OH H C OH H H C OH H Ribulose O C H Ribose Figure 5.3 Hexose sugars (C6H12O6) C Glyceraldehyde Ketoses • C H H Fructose • Monosaccharides – May be linear – Can form rings (about 65% of the time) O H 1C H HO 2 3 C 6CH OH 2 OH H C H 4 H H H C 5 5C 6 C H OH 4C OH OH OH O 5C H H OH C 6CH OH 2 3 C H 2C O H H 4C 1C CH2OH O OH H OH 3C 6 H 1C H 2C 4 HO H OH 3 OH H H 1 2 OH OH H H O 5 OH OH H Figure 5.4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. • Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage • Examples of disaccharides (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. CH2OH CH2OH H O H OH H OH HO H H H HO H OH H OH H H OHOH H O H OH H CH2OH H 1–4 1 glycosidic linkage HO 4 O H H OH H OH O H OH H H OH OH H2O Glucose Glucose CH2OH H (b) Dehydration reaction in the synthesis of HO sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. Figure 5.5 O CH2OH O H OH H H CH2OH H OH HO CH2OH O H H H HO CH2OH OH OH Maltose H O H OH H 1–2 glycosidic 1 linkage H Fructose 2 H H CH2OH OH H OH Sucrose H HO O HO H2O Glucose CH2OH O Polysaccharides • Polysaccharides Are polymers of sugars – Serve many roles in organisms • Starch Is a polymer consisting Chloroplast Starch entirely of glucose monomers – In plants, the starch is amylose or amylopectin, such as in potatoes. – In animals, the starch is glycogen, stored in the liver and muscles. 1 m Amylose Amylopectin Figure 5.6 (a) Starch: a plant polysaccharide • Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals Mitochondria Glycogen granules 0.5 m Glycogen Figure 5.6 (b) Glycogen: an animal polysaccharide Structural Polysaccharides • Cellulose Is a polymer of beta glucose H CH2O H O H OH H H 4 H OH HO H O CH2O H H O OH H 4 1 OH H HO H C OH glucose H C OH HO C H H C OH H C OH H C OH H OH glucose (a) and glucose ring structures CH2O H O CH2O H O HO 4 1 OH O 1 OH 4 O 1 OH OH OH CH2O H O CH2O H O O 4 1 OH O OH OH (b) Starch: 1– 4 linkage of glucose monomers CH2O H O HO Figure 5.7 A–C OH CH2O H O OH O 1 4 OH O OH OH O OH O O CH2O CH2O OH OH H H (c) Cellulose: 1– 4 linkage of glucose monomers OH – Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5.8 OH CH2OH OH CH2OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer Cellulose molecules A cellulose molecule is an unbranched glucose polymer. • Cellulose is difficult to digest – Cows (and termites) have microbes in their stomachs to facilitate this process Figure 5.9 An Animal Structural Polysaccharide • Chitin, is an important structural polysaccharide in animals – Is found in the exoskeleton of arthropods – Can be used as surgical thread CH2O H O OH H H OH H OH H H NH C O CH3 (a) The structure of the (b) Chitin forms the exoskeleton of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5.10 A–C in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Carbohydrates Review Lipids: Fats, Waxes, Oils • Concept 5.3: Lipids are a diverse group of hydrophobic molecules • Lipids Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic • Fats – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Fats H H C O C OH HO H C OH H C OH H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H Fatty acid (palmitic acid) H Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage O H H C O C H C H O H C O C O H C H Figure 5.11 O C H C H H C H C H H H C H C H H H C H H C H H C H H C H C H H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H (b) Fat molecule (triacylglycerol) H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H H C C H H H C H H C H H C H H C H H C H H C H H C H H H C H H H C H H H C H H • Fatty acids Vary in the length and number and locations of double bonds they contain • Saturated fatty acids Have the maximum number of hydrogen atoms possible: Have no double bonds Stearic acid Figure 5.12 (a) Saturated fat and fatty acid • Unsaturated fatty acids Have one or more double bonds – Can be converted to saturated via hydrogenation (pump-in hydrogens), forming trans-fats, or trans-fatty acids. Oleic acid Figure 5.12 (b) Unsaturated fat and fatty acid cis double bond causes bending Phospholipids • Phospholipids Have only two fatty acids Have a phosphate group instead of a third fatty acid • Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails” CH2 + N(CH ) 3 3 Choline CH2 O O P O– Phosphate O CH2 CH O O C O C CH2 Glycerol O Fatty acids Hydrophilic head Hydrophobic tails Figure 5.13 (a) Structural formula (b) Space-filling model (c) Phospholipid symbol The structure of phospholipids – Results in a bilayer arrangement found in cell membranes. They will spontaneously form into this structure when placed in water. • This happens because water is excluded from the hydrophobic regions and attracted to the hydrophilic. WATER Hydrophilic head WATER Hydrophobic tail Figure 5.14 Steroids: A type of Lipid (guaranteed answer on this year’s AP Exam!!) • Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings • One steroid, cholesterol Is found in cell membranes – Is a precursor for some hormones H3C CH3 CH3 Figure 5.15 HO CH3 CH3 • Concept 5.4: Proteins have many structures, resulting in a wide range of functions – Proteins • Have many roles inside the cell – – – – – Enzymes Channels, gates, receptors in membranes Signals (protein kinases) Transcription Factors And More!! • An overview of protein functions Table 5.1 • Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H2O Fructose H O 4 Products are released. Figure 5.16 3 Substrate is converted to products. Polypeptides • Polypeptides Are polymers of amino acids • A protein Consists of one or more polypeptides • Amino acids Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups • 20 different amino acids make up proteins CH3 CH3 H H3N+ C CH3 O H3N+ C H Glycine (Gly) O– C H3N+ C H Alanine (Ala) O– CH CH3 CH3 O C CH2 CH2 O H3N+ C H Valine (Val) CH3 CH3 O– C O H3N+ C H Leucine (Leu) H3C O– CH C O C O– H Isoleucine (Ile) Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H H3N+ C O– Methionine (Met) Figure 5.17 CH2 O C H CH2 O H3 N+ C C O– Phenylalanine (Phe) H O H2C CH2 H2N C O C O– H C O– Tryptophan (Trp) Proline (Pro) OH OH Polar CH2 H3N+ C CH O H3N+ C O– H Serine (Ser) C CH2 O H3N+ C O– H C CH2 O C H O– H3N+ C O H3N+ C O– H Electrically charged H3N+ CH2 C H3N+ O– C NH3+ O C CH2 C CH2 CH2 CH2 CH2 CH2 CH2 O CH2 C O– H H3N+ C O CH2 C H O– H3N+ C H O– H Glutamic acid (Glu) NH+ C O– Lysine (Lys) NH2+ H3N+ CH2 O CH2 H3N+ C H Aspartic acid (Asp) O C Glutamine (Gln) NH2 C C C Basic O– O O Asparagine (Asn) Acidic –O CH2 CH2 H Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH2 O C SH CH3 OH NH2 O NH CH2 O C C O– H O C O– Arginine (Arg) Histidine (His) Amino Acid Polymers • Amino acids – Are linked by peptide bonds Peptide bond OH CH2 SH CH2 H N H OH CH2 H C C H N C C OH H N C H O H O H (a) C OH O DESMOSOMES H2O OH DESMOSOMES DESMOSOMES SH OH Peptide CH2 bond CH2 CH2 H H N C C H O Figure 5.18 (b) Amino end (N-terminus) H H N C C H O N C C OH H O Carboxyl end (C-terminus) Side chains Backbone Determining the Amino Acid Sequence of a Polypeptide • The amino acid sequences of polypeptides is CRITICAL!! – Were first determined using chemical means – Can now be determined by automated machines • A protein’s specific conformation – Determines how it functions • Two models of protein conformation Groove (a) A ribbon model Groove Figure 5.19 (b) A space-filling model Four Levels of Protein Structure • Primary structure – Is the unique sequence of amino acids in a polypeptide +H N 3 Amino end GlyProThrGly Thr Gly Glu CysLysSeu LeuPro Met Val Lys Val Leu Asp AlaValArgGly Ser Pro Ala GluLle Asp Thr Lys Ser Tyr Trp Lys LeuAla Gly lle Ser ProPheHis GluHis Ala Glu Val AlaThrPheVal Asn lle Thr Ala Asp ArgTyr Ser Ala Arg GlyPro Leu Leu Ser Pro SerTyr Tyr Ser Thr Thr Ala Val Val Glu ThrAsnProLys o c – o Figure 5.20 Carboxyl end Amino acid subunits • Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet pleated sheet O H H C C N Amino acid subunits C N H R R O H H C C N C C N O H H R R O H H C C N C C N OH H R R R O R C H H R O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C H C O N H N C C H R H R N Figure 5.20 C C H H helix O H H C C N C C N OH H R O C H H H C N HC C N HC N C N H H C O C C O R R O R O C H H NH C N C H O C R C C O R R H C N HC N H O C • Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hyrdogen bond CH22 CH O H O CH H3C CH3 H3C CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond • Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits But What Holds all this Together?? Polypeptide chain Peptide Bonds Sulf-hydryl groups form disulfide bridges Hydrogen bonds If you remove all but the peptides, you lose the 2’, 3’, and 4’. Remove the peptides, lose it all. Collagen Chains Van der Waals forces Iron Heme Hydrophobic interactions Chains Hemoglobin Sickle-Cell Disease: A Simple Change in Primary Structure Primary structure Normal hemoglobin Val His Leu Thr 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Figure 5.21 Val His Leu Thr Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Pro Val Glu ... structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Pro Glul Glu Sickle-cell hemoglobin . . . Primary Quaternary structure subunit Function 10 m 10 m Red blood cell shape Exposed hydrophobic region Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. What Determines Protein Conformation? • Protein conformation Depends on the physical and chemical conditions of the protein’s environment • Denaturation Is when a protein unravels and loses its native conformation (notice the improper usage in this phrase? Good to avoid it). Denaturation Normal protein Figure 5.22 Denatured protein Renaturation The Protein-Folding Problem • Most proteins Probably go through several intermediate states on their way to a stable conformation • Chaperonins Are protein molecules that assist in the proper folding of other proteins Polypeptide Cap Correctly folded protein Hollow cylinder Chaperonin (fully assembled) Figure 5.23 Steps of Chaperonin Action: 1 An unfolded polypeptide enters the cylinder from one end. 2 The cap attaches, causing 3 The cap comes the cylinder to change shape in off, and the properly such a way that it creates a folded protein is hydrophilic environment for the released. folding of the polypeptide. Some Uses of Proteins • • • • • • • • Antibodies Enzymes Contractile Proteins Gene Regulation Receptor Proteins Sensory Proteins Signal Proteins Transport Proteins • Concept 5.5: Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleic acids The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) • Stores information for the synthesis of specific proteins • Directs RNA synthesis • Directs protein synthesis through RNA – Ribonucleic acid (RNA) DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Figure 5.25 Polypeptide Amino acids The Structure of Nucleic Acids • Nucleic acids Exist as polymers called polynucleotides •Each polynucleotide Consists of monomers called nucleotides 5’ end Nucleoside 5’C O Nitrogenous base 3’C O 5’C O O P O Phosphate group O Figure 5.26 3’C OH Figure 5.26 O O O 5’C CH2 (b) Nucleotide 3’ end (a) Polynucleotide, or nucleic acid 3’C Pentose sugar Nucleotide Monomers • Nucleotide monomers – Are made up of nucleosides and phosphate groups Nitrogenous bases Pyrimidines NH2 O O C C CH C 3 N CH C CH HN HN CH C CH C C CH N N O N O O H H H Cytosine Thymine (in DNA) Uracil (in RNA) Uracil (in RNA) U C U T Purines O NH2 N C C N CC NH N HC HC C CH N C N NH2 N N H H Adenine Guanine A G 5” Pentose sugars HOCH2 O OH 4’ H H 1’ 5” HOCH2 O OH 4’ H H 1’ H H H 3’ 2’ H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) Figure 5.26 (c) Nucleoside components Nucleotide Polymers • Nucleotide polymers Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next 5’ end 3’ end Sugar-phosphate backbone The sequence of bases along a nucleotide polymer Is unique for each gene Base pair (joined by hydrogen bonding) Old strands •Cellular DNA molecules Have two polynucleotides that spiral around an imaginary axis and Forms a double helix A 3’ end Nucleotide about to be added to a new strand 5’ end • The DNA double helix – Consists of two antiparallel nucleotide strands 3’ end 5’ end New strands 3’ end Itinerary For The Week • Tues., Wed, Fri. (9/10 – 9/13): Notes: Ch. 2-5 • Thurs-Fri: DO? • Fri: Thornton Wilder “It is a far, far better thing that I do, than I have ever done; it is a far, far better rest that I go to than I have ever known.” • Readings: – – – – P. 27: Familiarize 51 – 56 63 – 66 68 – 89 (as needed; should be very little) 73 Itinerary For The Day • Sidney Carton, as he comforted a young lady as they both were carted to the guillotine. • He saved Charles Darnay for Lucy. • Author????: 5/23/2017 74 Extra Help, Lab Time, Advisory Date Day of Week Day of Rotation Times 9/6 Friday 7 9:15 – 1:30 Notes Note: Whenever possible, get a pass the day BEFORE coming, and in ANY case, get a pass. Can’t make one of those times, please see me and we’ll work something out. Assignments, Tests, and Due Dates Assignment Due Date Agar Lab 9/6 Test: Ch. 2-5 ??