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Molecular Biology1Elements present in your body other than waterCarbon-30% of all biomass, original source of C is CO2 from photosynthesisHydrogenNitrogenOxygenPhosphorusSulfurIf carbon is present then the compound is considered organic.Carbon is the most versatile element b/c of its ability to bond to itself and other elements. It is tetravalent (4 bonds).If C and H are present it is a hydrocarbon: most are energy sources (fossil fuels)

2Molecules in living organisms: proteins, carbohydrates, lipids, nucleic acidsMost are polymers of smaller, covalently bonded, molecules called monomers.Functional groups: groups of atoms with specific chemical properties and consistent behavior.The consistent behavior of functional groups allows one to recognize the properties of molecules that contain them. i.e. polarity, electronegativity3Figure 3.1 Some Functional Groups Important to Living Systems (Part 2)

Amines- contain N, act as a base

Phosphates- involved in E transfers

Sulfur in sulfhydrls make disulfide bridges in protein4Figure 3.1 Some Functional Groups Important to Living Systems (Part 1)

Hydroxyls- act as an alcohol or polar

Aldehydes, Ketones, have one double bond to O

Carboxyls have two Os, one double, one single bond

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Functional groups serve important purposes in moleculesEstradiolTestosteroneMale lionFemale lion6Isomers

Structural isomer- same chemical formula, different arrangement of atoms.Structural Isomers7Figure 3.2 Optical Isomers

BioOptical IsomersSame chemical formula, arranged differently around an asymmetrical carbon8Biochemical UnityBiochemical unity-organisms can acquire needed biochemicals by consuming other organisms.Because all macromolecules have the same chemistry: The four biological molecules are present in the same proportions in all living things.Argument for common ancestor9Figure 3.3 Substances Found in Living Tissues

70% water10The function of macromolecules is directly related to their 3-D shape and their chemical properties/formula.This will determine molecular interactions such as solubility.11Synthesis QuestionQuestion: Carbon is an extremely important element to all life forms on the planet. Life on Earth, as we know it, could not exist without this element. In no more than three sentences, A) Identify the ultimate source of all Carbon for living organisms alive today and B)provide two brief explanations of why Carbon is important molecularly speaking.Scoring Rubric: 1pt. The ultimate source is CO2 from the atmosphere. 1pt. Discussion of source of carbon for making Carbohydrates, Lipids, Proteins, and Nucleic Acids.1pt. Discussion of the tetravalence allowing for a wide range of different molecules.1pt. Correct use of scientific terms. 1pt. Answer has no more than three sentences. (Following Directions.)

Molecular BiologyPolymers are formed in condensation reactions AKA dehydration synthesis.Condensation reactions result in monomers joined by covalent bonds. These require Ehttp://nhscience.lonestar.edu/biol/dehydrat/dehydrat.htmlThe reverse of a dehydration synthesis is hydrolysis reaction which break apart polymers and turn them into monomers.These make E

14Figure 3.4 Condensation and Hydrolysis of Polymers (A)

15Figure 3.4 Condensation and Hydrolysis of Polymers (B)

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Dehydration and HydrolysisReactionsShort polymerUnlinked monomerDehydration removes a watermolecule, forming a new bondDehydration reaction in the synthesis of a polymerLonger polymerHydrolysis adds a watermolecule, breaking a bondHydrolysis of a polymer17CarbohydratesSee the Carbonyls and Hydroxides?

18Carbohydrates (C,H,O 1:2:1)Molecules that contain carbons flanked by a H group and an OH group.Four major types of carbs: mono, di, poly, and oligo saccharides.Two major functions: Source of energy that can be released in a usable form to body tissuesServe as carbon skeletons for other 3 macromolecules.19MonosaccharidesProduced through photosynthesis.All living cells contain glucose.Most monosaccharides are in the D series of optical isomers (proteins are L)20Figure 3.13 Glucose: From One Form to the Other (Part 2)

21Figure 3.14 Monosaccharides Are Simple Sugars (Part 1)

22Figure 3.14 Monosaccharides Are Simple Sugars (Part 2)

Structural These are structural isomers.23Glycosidic LinkagesMonosaccharides covalently bind together in condensation reactions to form glycosidic linkages.Glycosidic linkages can be or .Examples of disaccharidessucrose table sugar = glucose + fructose lactose milk sugar = glucose + galactose maltose malt sugar = glucose + glucose

24Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages (Part 1)

25Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages (Part 2)

ThiThis is cellobiose, a subunit of cellulose, humans dont have the enzymes to break this down, but cows do. To us it is merely roughage.

Cellulose is a very stable glucose polymer, and is the principle component of cell walls.26Oligosaccharides (3-20)Often covalently bonded to proteins and lipids on cell surfaces and act as recognition signals.ABO blood groups27PolysaccharidesFormed by glycosidic linkages, animal and plant energy storage form.Three forms: starch, glycogen, cellulose, and chitin.Starch and glycogen easily hydrolyzed for energy.Starch- all contain alpha linkages, stored in plants.Cellulose- plant cell wall structure; most abundant organic molecule on earthGlycogen-energy storage in animalsChitin- found in exoskeletons and fungi cell walls28PolysaccharidesGlucose must be stored as glycogen because glycogen does not exert as much osmotic pressure on the cell as one glucose molecule

29Figure 3.16 Representative Polysaccharides (A)

30Carbohydrate Energy Storage

31Figure 3.16 Representative Polysaccharides (B)

Cellulose, Starch, & Glycogen32Chemically Modified CHOsSome CHO can be modified by adding functional groups such as a phosphate or amino group.Phosphate sugars and amino sugars33Lipids C,H,OLipids are hydrocarbons that are insoluble in water because of their nonpolar, covalent bonds.All the extra H= 2x E of CHOHydrophobic.One lipid molecule consists of a glycerol (alcohol) bonded to 3 fatty acid chains.The fatty acids are held together through van der Waals forces not covalent bonds; therefore they are not true polymers.34LipidsThe bond that holds each fatty acid molecule to the glycerol is formed through dehydration synthesis, and is called an ester linkage.The ester linkage is a covalent bond.

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Ester Linkage and LipidsDehydration reaction in the synthesis of a fatGlycerolFatty acid(palmitic acid)36Math QuizTell if each pH or pOH is an acid, base, or neutral by writing ACID, BASE, or NEUTRAL on the line next to the prompt. (1 points each)pH 3 ____________ pOH 7 ______________ pH 14 _______________ pH 7 ____________pH 4 ______________pOH 0 ______________pOH 14 ____________ pOH 9 _____________pOH 2 ____________ pH 10 _____________

Calculate pH differences in H concentrationpH 2- pH 5

pH 1- pH 2

pH 3- pH 8

pH 7 pH 10

pH 1- pH 14pH 1- pH 3

pH 10- pH 14

pH 3- pH 7

pH 5 pH 10

pH 1- pH 11

Figure 3.18 Synthesis of a Triglyceride

39Lipid FunctionsFats and oils store energyPhospholipids in cell membrane for structureCarotenoidsHormones and vitaminsFat = insulation (Camels)Lipids coat neurons for electrical insulationOil and wax on skin surface repel water

40LipidsOne lipid unit is called a triglyceride/triglycerol.Triglycerides solid at room temp. are fats.Saturated fatty acid- all C-H bonds are singleAnimal fat, least healthy.Triglycerides liquid at room temp. are oils.Unsaturated fatty acid (mono, poly) some of the C-H bonds are double causing kinking in the hydrocarbon chain.Plant oils, lower melt. pt., healthier

Polyunsaturated Fats- many double bonds, usually in plantsHydrogenated or Trans Fat- Unsaturated turned saturated

41Saturated vs. Unsaturated

42Figure 3.19 Saturated and Unsaturated Fatty Acids

43PhospholipidsA phosphate molecule bonds to the glycerol replacing one hydrocarbon chain (fatty acid).Since phosphate functional group is (-) it is hydrophilic and attracts polar H20 molecules.In aqueous environment, phospholipids line up with hydrophobic region tails on one end, and hydrophilic heads on the other.Phospholipids form a bilayer.44Figure 3.20 Phospholipids (A)

45Figure 3.20 Phospholipids (B)Phospholipid bilayers form biological membranes.

46Waxes

47Steroid Structure

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LE 4-9EstradiolTestosteroneMale lionFemale lion49Cell Membranes

50Lipid storage

51Energy and Macromolecules Data Set 6

52Proteins- suffix lin eg insulinContain: C, H, O, N, P, and SProtein monomers are known as amino acids, which then fold into the polypeptide form of proteins.50% of organisms biomass

53Essential Amino AcidsOver 20 amino acids11 non-essential9 essential

These 9 are essential because they cannot be synthesized by the body and must be supplemented.Phenyalanine Valine Threonine Tryptophan Isoleucine Methionine Leucine Lysine Histidine54Protein StructureCan be made of more than one polypeptide chainThe sequence of amino acids in each polypeptide chain is the source of diversity in protein structure and function.

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What Are the Chemical Structures and Functions of Proteins?Amino acids have carboxyl and amino groupsthey function as both acid and base.Rgroup= property

56These hydrophylic amino acids attract ions of opposite charges.

Table 3.2 (Part 1)57Hydrophylic amino acids with polar but uncharged side chains form hydrogen bondsTable 3.2 (Part 2)

58Table 3.2 (Part 3)Hydrophobic amino acids

59Table 3.2 (Part 4)

60ProteinsAmino acids bond together covalently by peptide bonds to form the polypeptide chain.The beginning of all polypeptides begin with the amino group of an amino acid: the N terminus and the end of the chain is the carboxyl group: the C terminusNC orientation61Figure 3.6 Formation of Peptide BondsThe peptide bond is inflexibleno rotation is possible.

62Protein StructurePrimary Structure-sequence of amino acids in the polypeptide chain. Peptide backbone N-C-C.Secondary Structure- determined by hydrogen bonds, alpha helix and beta pleated. Bonds between amino (H) and carboxyl (C and O)Tertiary Structure- additional folding between the R groups (side chains). Folded by disulfide bridges, cysteine has the sulfur.Quarternary Structure- result from subunits (separate tertiary structures) folding together. Multiple polypeptides together.

63Figure 3.7 The Four Levels of Protein Structure (A)

64Figure 3.7 The Four Levels of Protein Structure (B, C)

65Figure 3.7 The Four Levels of Protein Structure (D, E)

66Primary (1) sequence

67Primary Structure is IMPORTANT

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Sickle Cell and Oxygen transportPrimarystructureSecondaryand tertiarystructures123Normal hemoglobinValHisLeu4Thr5Pro6GluGlu7PrimarystructureSecondaryand tertiarystructures123Sickle-cell hemoglobinValHisLeu4Thr5Pro6ValGlu7QuaternarystructureNormalhemoglobin(top view)aaaaFunctionMolecules donot associatewith oneanother; eachcarries oxygen.QuaternarystructureSickle-cellhemoglobinFunctionMolecules interact withone another tocrystallize intoa fiber; capacityto carry oxygenis greatly reduced.Exposedhydrophobicregionb subunitb subunit692 structure

703 Structure

714 Structure

72Proteins Natural Form

73Protein FunctionStructural supportProtectionTransport Catalysis- speeding up a chemical reaction Defense Regulation Movement

74Protein denaturationDenaturation= loss of 3-D shape and function (unfold due to environmental stressors)Proteins are sensitive to their environment due to weaker bonds in the 2nd and 3rd structure. 3 Denaturing factors:Increased temperatureAlterations in pHSalt concentration changesDenaturation is usually irreversible75Figure 3.11 Denaturation Is the Loss of Tertiary Protein Structure and Function

76Protein ShapeSometimes proteins will bind to the wrong ligand (molecule) while completing their folding process. E.g. alzheimersChaperonins- type of protein that prevents misfolding.

77EnzymesEnzymes are proteins that are catalysts that speed up chemical reactions in cells.Words that end in ase are enzymesEnzymes form an enzyme-substrate complex Animation: How Enzymes Work

78Nucleic Acids- C,H,O,P,NNucleic acids are polymers designed for storage, transmission, and use of genetic information.DNA & RNADNA encodes our heredity info.DNA contains the info, uses RNA to create an amino acid sequence (proteins) which carry out lifes functions.Pyrimidines: cytosine, thymine, uracilPurines: adenosine, guanine79NucleotideNucleotides are the monomers for nucleic acids.Each nucleotide consists of a pentose sugar, phosphate group, and nitrogenous base.Nitrogenous bases can be pyrimidines (single ring) or purines (2 fused rings)Pyrimidines-C,T,UPurines-G, A803.5 What Are the Chemical Structures and Functions of Nucleic Acids?DNAdeoxyriboseRNAribose

81DNA & RNA BackboneAlternate pentose sugar and phosphate groups (S-P-S-P-S-P)The nitrogen bases project off the backbone.Nucleotides bonded by phosphodiester linkages.Phosphodiester linkages form between the sugars linked by the phosphate.82Figure 3.24 Distinguishing Characteristics of DNA and RNA (Part 1)

83DNAHydrogen bonds link nitrogenous bases together.Base pairing rule-purine and pyrimidine always pair up.A-T and C-G in DNAA-U and C-G in RNAKnow why base pairing is complimentary p.5984Figure 3.24 Distinguishing Characteristics of DNA and RNA (Part 1)

85DNA RelationshipsDNA in all organisms, chimps and humans share 98% base sequence with humans.Scientists use DNA to determine evolutionary relationships.Nucleotides also are used in energy reactions. (ATP and GTP).Nucleotides are used in hormones and the nervous system (cAMP).86HW: Due Friday 8-30-13Macromolecule TypeName of MoleculeSourceRole in Organisms (What does it do?)5 CarbohydratesglucoseplantsImmediate energy5 Lipids5 Proteins4 NucleotidesHow did life begin?Could life have come from outside earth?Allan Hills region of Antartica, meteorite from MarsMiller and Urey experiment 1953- chemical evolution. Took inorganic substances and made them organicMiller and Urey ExperimentRNA world before DNA- RNA less stable than DNARNA ribozymes could replicate itselfRibozymes are responsible for peptide bonds88Figure 3.27 Was Life Once Here?

89Energy Source- Stanley Miller

90Figure 3.28 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 1)

914 Steps for Life to Emerge on Earth1. Abiotic synthesis of amino acids and nucleic acids.2. Monomers must join to make polymers3. RNA/DNA form and gain ability to reproduce and stabilize using bonds and complimentary bonding.4. Evolution of the protobiont first life formEvidence for #1: Abiotic synthesisMiller and Urey- hypothesized about early earths organic compositionH2, CH4, NH3 and H2O vaporThese things formed amino acids and oilsThe compounds came from volcanic eruptions and the energy from lightningThese compounds collected in the oceans and wala life

Evidence for #2: PolymerizationResearchers have taken fools gold, sand, and clay, and exposed to it to intense heatIn the presence of water (tides) amino acids and oils become polymersEvidence for #3: RNA/DNASome RNA can act as ribozymes that act as great info storage binsOver time it is believed RNA evolved into a more stable DNAEvidence for #4: Protobiont FormationExperiments show that lipids and other molecules can form membranes (cell)Over millions of years they become prokaryotic cellsRepresentation of a Protobionts

97Data Set Question (U1,D3)

Question: In no more than three sentences, explain why the abiotic synthesis of the nucleic acids RNA and DNA was overall so essential to helping generate life on Earth? (5 Points)

Synthesis Question (U1, D3)Question: In no more than three sentences, explain why the abiotic synthesis of the nucleic acids RNA and DNA was overall so essential to helping generate life on Earth? (5 Points)1pt. Discussion of the ability to store molecular information on the construction of molecule1pt. Discussion of inheritance of information from one generation to the next1pt. Discussion of the long term stability of DNA1pt. Correct use of scientific terms.1pt. Answer has no more than three sentences. (Following Directions.)