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LIFE 102 Week 2

by: Kyla Tovar
Kyla Tovar
GPA 3.6

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Lecture notes from Monday, Wednesday, and Friday, as well as notes from the assigned readings for chapter 4 and 5.
Attributes of Living Systems
Jennifer L Neuwald
Class Notes
Biology, Molecules, DNA, RNA
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This 16 page Class Notes was uploaded by Kyla Tovar on Friday September 2, 2016. The Class Notes belongs to Life 102 at 1 MDSS-SGSLM-Langley AFB Advanced Education in General Dentistry 12 Months taught by Jennifer L Neuwald in Fall 2016. Since its upload, it has received 31 views. For similar materials see Attributes of Living Systems in Life Sciences at 1 MDSS-SGSLM-Langley AFB Advanced Education in General Dentistry 12 Months.


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Date Created: 09/02/16
Chapter 4: Carbon and the Molecular Diversity of Life I. Carbon: The Backbone of Life a. Carbon enters the biosphere through the action of plants and other photosynthetic organisms b. Ability to form molecules, that are large, complex, and varied, making possible the diversity of organisms that have evolved on earth c. Carbon accounts for the variety of biological molecules II. Organic Chemistry is the Study of Carbon Compounds a. Organic chemistry: the study of carbon compounds b. Physical and chemical laws govern the processes of life c. Organic compounds range from simple molecules to colossal ones d. Organic Molecules and the Origin of Life i. Complex organic molecules could arise spontaneously under conditions throughout at that time to have existed on the early earth ii. Carbon has the ability to form 4 bonds iii. Diversity possible because of the unique chemical veracity of the element carbon III. Carbon Atoms Can Form Diverse Molecules by Bonding to Four Other Atoms a. Key to atom’s chemical characteristics is its electron configuration i. Determines the kinds/number of bonds b. The Formation of Bonds with Carbon i. 6 electrons in carbon, 2 in the first shell, 4 in the second ii. Usually form single or double covalent bonds iii. The electron configuration of carbon gives it covalent compatibility with many different elements iv. H, O, N, C are basis for covalent bonding in chemistry v. CO2 simple and lacks Hydrogen, considered inorganic c. Molecular Diversity Arising from Variation in Carbon Skeletons i. Carbon chains form the skeletons of most organic molecules ii. Variation in carbon skeleton is important source of the molecular complexity and diversity that characterize living matter iii. Hydrocarbons: organic molecules consisting of only carbon and hydrogen 1. Major components of petroleum (fossil fuel) 2. Not present in most living organisms 3. Undergo reactions that release a relatively large amount of energy iv. Isomers: compounds that have the same numbers of atoms of the same element but have different structures, hence different properties 1. Structural isomers: differ n the covalent arrangement of their atoms a. The number of possible isomers increase as carbon skeleton increase in size b. Differ in location of double bonds 2. Cis-trans isomers: carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds a. Subtle difference in shape between isomers can dramatically affect the biological activities of organic molecules 3. Enantiomers: isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon v. Asymmetric carbon: one that is attached to four different atoms or groups of atoms vi. “right-handed” versions won’t fit into the same space as the “left-handed_ 1. only one is active at a time IV. A few Chemical Groups are Key to Molecular Function a. Properties depend on chemical groups attached to the skeleton b. The chemical groups most important in the processes of life i. Functional groups: chemical groups directly involved n chemical reactions ii. Seven chemical group most important 1. Hydroxyl 2. Carbonyl 3. Carboxyl 4. Amino 5. Sulfhydryl 6. Phosphate 7. Methyl a. All but methyl are chemically reactive, all except sulfhydryl and methyl are hydrophilic iii. ATP: An Important Source of Energy for cellular processes 1. ATP: function in the cell is important, complicated organic phosphate 2. Said to store energy a. More accurate: storing the potential to react with water iv. The Chemical Elements of Life: A Review 1. Carbon is the virtuoso of the covalent bond Monday Lecture  Acidity: Hydrogen ions in a solution  In pure water, H+ and OH- concentrations are equal: o (H+)=(OH-)=10^-7 M  Dissociation: ability to form other molecules  #H+>(H+)…(OH-) implied, measure of (H+) is the same as (OH-)  pH=-log(H+)…1pH=10x difference, 1 change in pH, creates a 10x difference o Ex: pH5=10x H+ vs. pH6, ph5=100x H+ vs. pH7  Higher (H+)… ore acidic; lower pH  Lower (H+)…more basic; higher pH  pH scale: 0-14 o pH 7= neutral o pH<7 = acidic o pH>7 = basic  Where do the H+ or OH- from o Acid more H+ o Bases less H+  Buffers= minimizes changes in OH- and H+ o Stability in pH is critical for cells o H2CO3 if pH rises turn into HCO3^- + H^+ o No buffer=acidification  Carbon which is 18.5%  Carbon is the element of life  Organic Chemistry: carbon based molecules o Carbon molecules can be simple or complex  C is tetravalent: can make 4 covalent bonds o Form a tetrahedral shape, critical for function of molecules  Single bonds will always form a tetrahedral  Double bonds are on a single plane  Molecular Diversity: (1) Carbon Chain Length o Hydrocarbons: 2 types of atoms, carbon, and hydrogen  Molecular Diversity: (2) Carbon Chain Branching o Changes structure, molecular formula same, results in different function  Molecular Diversity: (3) Double Bond Position o Change where the double bond appears  Molecular Diversity (4): Rings  Isomers: some atoms, different structure o Structural isomers: differ in covalent bond partners o Cis-trans isomers: same covalent bond partners, but different spatial arrangement  Cis isomer: same side  Trans isomer: opposite side o Enantiomers: Asymmetric distribution of atoms and carbon=mirror image  Right molecule will not fit into left molecule, think of gloves o A small number o chemical groups are key to the functioning of biological molecules  Carbon skeleton with hydrocarbon o X is called a functional group, or side chain  Usually O, N, H, S, and P o 7 functional groups most important for life 1. Hydroxyl Group (--OH) a. Compound Name=Alcohol b. Polar; Hydrophilic; Can Ionize i. If polarity is hydrophilic 2. Carbonyl Group (C_-O) a. Compound name=ketone or Aldehyde i. Ketone is the middle ii. Aldehyde is the end b. Polar; Hydrophilic; Hard to Ionize 3. Carboxyl Group (-COOH) a. Compound Name=Carboxylic Acid b. Polar; Hydrophilic; Easy to Ionize c. Acts as an Acid can donate H+ 4. Amino Group (--NH2) a. Compound Name=Amino b. Polar; Hydrophilic; Easy to Ionize c. Acts as a Base can remove H+ 5. Sulfhydryl Group (--SH) a. Compound Name= Thiol b. Polar; Hydrophilic; Can Ionize i. Molecules may have multiple, functional group 6. Phosphate Group (--OPO3^-2) a. Compound Name= Organic Phosphate b. Polar; Hydrophilic; Ionized Chapter 5: The Structure and Function of Large Biological Molecules  The molecules of Life o All-important large molecules sorted into classes called carbohydrates, lipids, proteins, and nucleic acids o Macromolecules: huge and include carbohydrates, proteins, and nucleic acids  The architecture of a large biological molecule plays an essential tale in its function I. Macromolecules are Polymers, Built from Monomers a. Polymer: a long molecule consisting of many similar or identical building blocks linked by covalent bonds i. Include carbohydrates, proteins, and nucleic acids b. Monomers: the repeating units that serve as the building blocks of a polymer are smaller molecule c. The Synthesis and Breakdown of Polymers i. Cells make and make polymers are the same ii. Enzymes: specialized macromolecules that speed p chemical reactions iii. Monomers connected by reaction in which two molecules are covalent bonds, with the loss of a water molecule 1. Called dehydration reaction iv. Hydrolysis: a process that is essentially the reverse of the dehydration, means water breakage 1. Ex; digestion d. The Diversity of Polymers i. Small variations in polymers, in DNA and proteins ii. Constructed from 40-50 common monomers iii. The key is arrangement II. Carbohydrates: Include sugar and Polymers of Sugar a. Carbohydrates: include sugar and polymers of sugar b. Simplest are monosaccharides c. Carbohydrates macromolecules are polymers called polysaccharides d. Sugars i. Monosaccharides: generally, have molecular formulas that are same multiple of the unit CH2O ii. Sugar is aldose (aldehyde sugar) or a ketose (ketone sugar) iii. Criterion for classifying sugars is the size of the carbon skeleton iv. Monosaccharides are major nutrients for cells v. Disaccharide: consists of two monosaccharides joined by a glyosidic linkage vi. Glyosidic linkage: a covalent bond formed between two monosaccharides by a dehydration reaction e. Polysaccharides i. Polysaccharides: macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycolic linkages ii. Serve as storage material or building material iii. Architecture and function determined by its sugar monomers and the position of its glycosylic linkages iv. Storage polysaccharides 1. Plants use starch a. Starchy: a polymer of glucose monomers 2. Most of the glucose monomers in starch are joined by 1-4 linkages 3. Simplest form of starch, amylose, is unbranched 4. Glycogen: stored by animals, a polymer of glucose that is like amylopectin but more extensively branched v. Structural polysaccharides 1. Cellulose: major component of the tough walls that enclose plant cells 2. Glucose can form a ring 3. Few organisms can digest cellulose 4. Not a nutrient for humans but part of a healthful diet 5. Chitin: the carbohydrate used by anthropoids to build their exoskeletons a. B linkages like cellulose III. Lipids are a Diverse group of Hydrophobic Molecules a. Do not include polymers b. Generally, not big enough to be considered macromolecules c. Lipids: grouped with each other because they share the important trait of mixing poorly, if at all, with water d. Consist of hydrocarbon regions e. Fats i. Not polymer, they are large molecules assembled from smaller molecules by dehydration reactions ii. Fat: constructed from two kinds of smaller molecules: glycerol and fatty acids f. Fatty acid: long carbon skeleton, usually 16 or 18 carbon atoms in length g. Fats separate from water because the water molecules hydrogen bond to one another and exclude the fats h. Triaclyglycerol: bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group, consist of three fatty acids linked to one glycerol molecule i. Saturated fats and unsaturated fats refer to the structure of the hydrocarbon chains of the fatty acids j. Saturated fatty acid: structure solid to be saturated with hydrogen, resulting fatty acid k. Unsaturated fatty acid: one or more double bonds with one fewer hydrogen atom on each double-bonded carbon l. Saturated fats are solid at room temp m. Unsaturated fats are liquid at room temp n. Diet rich in saturated fats may contribute to cardiovascular diseases o. Trans fat: trans double bond p. Major function of fats is energy storage IV. Phospoholipids a. Cells could not exist without it b. Essential because they are major constitutions of cell membranes c. Phospholipids: similar to a fat molecule but has only two fatty acids attached to glyceride rather than three d. Hydrocarbon tails are hydrophobic and excluded from water e. Hydrophilic head that has an affinity for water f. Form bilayer with heads facing water and tails in between V. Steroids a. Steroids: lipids characterized by a carbon skeleton consisting of four fused rings b. Cholesterol: a type of steroid, crucial molecule in animals VI. Proteins include a diversity of structures, resulting in a wide range of functions a. Every dynamic function of living being depends on proteins b. Account for 50% of the dry mass of most cells c. Speed up chemical reaction, defense, storage, transport, cellular communication, movement, or structural support d. Catalyst: chemical agents that selectively speed up chemical reactions without being consumer by the reaction e. Proteins constructed from 20 amino acids f. Polypeptide: the bond between amino acids is called a peptide bond, so a polymer of amino acids is this g. Protein: biologically functional molecule made up of one or more polypeptides, each facade and called into a specific three- dimensional structure h. Amino Acid Monomers i. Amino acid: an organic molecule with both an amino group and a carboxyl group 1. At the center there is an asymmetric carbon atom called the alpha (a) carbon 2. 4 partners: amino group, carboxyl group, a hydrogen atom, and a variable group side-chain ii. enzymatic protein 1. Function: selective acceleration of chemical reactions iii. Defensive proteins 1. Function: protection against diseases iv. Storage proteins 1. Function: storage of amino acids v. Transport proteins 1. Function: transport of substances vi. Hormonal Proteins 1. Function: coordination of an organism’s activities vii. Receptor proteins 1. Function: responses of cell to chemical stimuli viii. Contractile and Motor Proteins 1. Function: movement ix. Polypeptides (Amino Acid Polymers) 1. Two amino acids can be joined by a dehydration reaction a. Peptide bond: resulting covalent bond 2. Chemical nature determined by kind and sequence of side chains i. Protein Structure and Function i. Many proteins are roughly spherical (globular proteins) ii. Fibrous proteins: shaped like long fibers iii. Four Levels of Protein Structure 1. Share primary, secondary, and tertiary structure 2. Quaternary structure arises when a protein consists of two or more polypeptide chains iv. Sickle-cell disease: an inherited blood disorder, is caused by the substation of one amino acid for the normal one at a particular position in the primary structure of hemoglobin j. What determines protein structure? i. A polypeptide chain of a given amino acid sequence can be arranged into a three-dimensional shape determined by the interactions responsible for secondary and tertiary structure ii. Denaturation: protein to unravel and lose its native shape 1. Transferred from aqueous environment to nonpolar solvent 2. Excessive heat iii. The sequence of amino acids determine shape k. Protein folding in the cell i. Several intermolecular structures on way to stable shape ii. Chaperonin: protein molecules that assist in the proper folding of other proteins iii. Misfolding is a serious problem iv. X-ray crystallography: used to determine the 3-D structure of many other proteins VII. Nucleic Acids Tore, Transmit, and Help express Hereditary Information a. Primary structure determined by the amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance aka gene b. Nucleic acids: polymers made of monomers called nucleotides c. The roles of nucleic acids i. DNA provides directions for its own replication and directs RNA synthesis ii. Gene expression: DNA to RNA to Protein synthesis d. The components of Nucleic Acid i. Polynucleotides: nucleic acids are macromolecules that exist as polymers ii. Nucleotide: each polynucleotide consists of monomers 1. Three parts; a five carbon sugar (pentose), nitrogenous base and one or more phosphate group 2. Polynucleotide each monomer has one phosphate group 3. Each nitrogenous base has one or two rings 4. Pyrimidine: one six-membered ring of carbon and nitrogen atoms a. C (cytosine), T (thymine), and U (Uracil) 5. Purines: larger, with a six-membered ring fused to a five-membered ring a. A (adenine), and G (guanine) 6. Thymine only in DNA 7. Uracil only in RNA 8. Deoxyribose: the sugar in DNA 9. Ribose: the sugar in RNA 10. Deoxyribose lacks an oxygen atom on its second carbon ring e. Nucleotide Polymers i. Sugar-phosphate backbone ii. A gene’s meaning to the cell is encoded in its specific sequence of the four DNA bases f. The structures of DNA and RNA molecules] i. Double helix: the two sugar phosphate backbones in opposite directions ii. Antiparallel= double helix iii. Two strands help together by hydrogen bonds between the paired bases 1. A=T and G=C iv. RNA exists as a single strant 1. A=U and G=C VIII. Genomics and Proteomics have transformed biological inquiry and applications a. 1970s study of genes b. genomics: study of problems by analyzing large sets of genes or even comparing whole genomes of different species c. proteomics: a similar analysis of large sets of proteins d. DNA and proteins of Tape Measures of Evolution Wednesday Lecture 7. Methyl Group (--CH3) a. Compound name=Methylated ‘X’ b. Non Polar; Hydrophobic; No Ionization  Polar water molecules are not interested in it  Important with steroids  Macro= big, molecules o 1. Carbohydrates o 2. Lipids o 3. Proteins o 4. Nucleic Acids  molecular structure determines function  What makes a macromolecule? o Polymers, built from monomers o Monomers to polymers by dehydration o Polymers to monomers by hydrolysis o Reactions occur in an aqueous solution o Dehydration  1. Remove H= OH (H2O)  2. New bond is formed  3. Polymer is made o Hydrolysis  1. Split H2O (into H+ OH)  2. H+ OH attach to polymer  Polymer bond is broken  -lysis: to break  monomers= unity of life o 40-50 kinds 1.Carbohydrates  structure= monomer= monosaccharides o sugar= (CH2O)n o How do sugar molecules vary?  (a) Location of Carbonyl Group  (b) Length of Carbon Backbone  (c) Spatial arrangement  isomers o rings of sugar o disaccharids= 2 monosaccharides o dehydration reaction creates covalent bond o structure: polysaccharides (can have >100 k units)  combination of monomers  hydroxyl group position o function of polysaccharides: (a) Energy Storage  starch: plant storage polysaccharide  glycogen: animal storage polysaccharide  take energy and release energy o (b) Structural support  cellulose: plant structural polysaccharide  most animals cannot digest cellulose exoskeletons in animals  chitin: animal and fungi structural polysaccharide 2.Lipids  structure o not polymers o are formed from small molecules via dehydration o hydrophobic (insoluble in water) o Three types of lipids:  (a) Fats  (b) Phospholipids  (c) Steriods  Fats o Structure= fatty acids (linked to glycerol) o Functon= energy storage (also cushioning, insulation) o Dehydration reactions: attaches fatty acid tail o ‘Complete’ Fat: Triacylglycerol o Saturated: al the carbon atoms have as many hydrogen atoms as they can hold ( no double bonds)  Solid at room temperature  Found in animal fat o Unsaturated: 2+ of the carbons have at least 1 double bond  Liquid at room temperature  Found in plant oil and fish oil  The double bond causes a bend so the lipids are farther apart  (b) Phospholipids: o Structure  2 fatty acids  Phosphate group  Glycerol o Amphipathic has ends with both…  Polar (hydrophilic): head  Non-polar (hydrophobic): tail (hydrocarbon) o Function: cell membrane  Form bilayer, head out towards water, with tail pointing inside, in order for tail to avoid water\  What allows for cell membrane to form  (c) Steriods o structure: 4 carbon rinds and side groups o function: signaling (hormones) and membrane fluidity  critical inside cell membrane for fluidity 3. Proteins  Structure: Monomers= Amino Acid o R= The rest of the molecule or a variable group  20 different amino acids occur in proteins, each with a different ‘R’ group o only the side chains differ  polymer=polypeptide  Levels of protein structure o 1. Primary  linear chain of amino acids o 2. Secondary  coil and fold polypeptide backbone  hydrogen bonds between polypeptides not side chains, a helix, b pleated sheet o 3. Tertiary  interactions between ‘R’ groups  Types of interactions  Hydrophobic (not a bond)  Ionic bonds  Covalent disulfide brides  Hydrogen bonds o 4. Quaternary  2+ polypeptides  not all proteins have 4 structure o Structure= (1) environment (2) Chaperonins o 1. Enzymes  accelerate chemical reactions o 2. Storage  store amino acids o 3. Hormonal  coordinate organism’s activities o 4. Contractile/ Motor  movement o 5. Defensive  `immunity- protect against disease o 6. Transport  transportation of substances o 7. Receptor  response of cell to chemical stimuli o 8. Structural  support o Sickle Cell Anemia: What happens when you change the structure  Proteins do not associate with one another, each carries oxygen  Proteins aggregate into a fiber, capacity to carry oxygen is reduced 4. Nucleic Acids  Structure: Monomers= Nucleotides o Nucleotide  Phosphate group  Pentose sugar  Nitrogenous base  Structure: pentose sugars of nucleotide o DNA: deoxyribonucleic acid o RNA: Ribonucleic acid  Structure: Nitrogenous Bases of the Nucleosides  Structure: Deoxyribonucleic Acid (DNA) o Double helix o Hydrogen bonds for stability o 1) Complementary  if you know the nucleotide on one other side, you can infer the other side  crucial for replication o 2) Anti-parallel  strands run in opposite directions  5’= Phosphate Group  3’ Hydroxyl Group  Structure: Ribonucleic Acid (RNA) o Single stranded  But can loop back on itself and pair  Base pair joined by hydrogen bonding  Function: Carry genetic information o Blueprint of the cell o DNA directs RNA synthesis o RNA directs protein synthesis


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