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BSC 2010 Week one and two notes.

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BSC 2010 Week one and two notes. BSC2010

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These notes cover everything said and or mentioned in class over the past two weeks.
Integrated Principles of Biology 1
Gillooly,James FMiyamoto,Michael MasaoOppenheimer,David G
Biology, cells, atoms, Origin of life
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"What an unbelievable resource! I probably needed course on how to decipher my own handwriting, but not anymore..."
Cordelia Pacocha

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This 13 page Bundle was uploaded by Valerie Notetaker on Sunday January 17, 2016. The Bundle belongs to BSC2010 at University of Florida taught by Gillooly,James FMiyamoto,Michael MasaoOppenheimer,David G in Fall 2015. Since its upload, it has received 62 views. For similar materials see Integrated Principles of Biology 1 in Biology at University of Florida.


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Date Created: 01/17/16
BSC2010 NOTES 1/6/2016 Class one: introduction Class broken up into three sections: - Cells - Genetics - Evolution Instructor - Dr. Sixue Chen - Office hour location: 521 Carr Hall - Office hours: Monday and Wednesday period 7 (1:55 PM TO 2:45 PM) OR BY appointment Everything is due Feb 9 th Chapter one principles of life. *Concept 1.5 science is based on Quantifiable observations and experiments - Scientific investigations are based on observation and experimentation o Science is Based on human curiosity. - Observation is enhanced by technology: microscopes imaging, genome sequencing and satellites. o Technology drives science to move forward. - Observations must be qualified by measurement and mathematical and statistical calculations. - Inductive reasoning allows one to make to general conclusion based on limited set of observations. - These general conclusions allow the scientist to predict that the same results will be obtained in the future under similar circumstance. - Inductive reasoning example: o Observation:  I have observed that the sun rises in the east and sets in the west every day for the past month. o Generalization/ prediction:  I predict that the sun will rise in the east and set in the west every day. - Question: o why does the sun rise in the east and set in the west? - Hypothesis: o The tentative explanation I have is that the earth is rotation relative to the sun o You need to have a testable hypothesis. - Experiment: o To test this I will use a pendulum to try and observe the effects of the earth rotating. - Deductive reasoning: o Knowing the laws of motion , and believing them to be true, o If I start a pendulum moving, it will move I hand ever changing are arc if the earth rotates under it. o Alternatively, if the earth does not rotate, then the arc traced by the pendulum will not change direction. o Show that the world is rotating with the pendulum - Scientific method: o Observation o Questions o Hypothesis o Predictions o Tests of the predictions. (experiments) - The role of hypotheses in inquiry o Observation: your flashlight doesn’t work o Question: why doesn’t your flashlight work?  Hypothesis 1: the batteries are dead  Hypothesis 2: the bulb is burnt out - Both of these hypotheses are testable. - A closer Look at Hypotheses in Scientific inquiry and limitation: o Must be testable o Hypothesis based science often makes use of two or more alternative hypotheses o Failure to falsify a hypothesis does not prove that hypothesis o For example, you replace your flashlight bulb, and it now works; this supports the hypothesis that your bulb was burnt out, but does not prove it (perhaps the first bulb was inserted incorrectly) o In science, observation and experiments must be repeatable. o Science cannot support or falsify supernatural explanations, which are outside the bounds of science. - Limitation of science: o In science, observations and experimental results must be repeatable o Science cannot support or falsify supernatural explanations which are outside of the bounds of science. *Part one: Cells - Atoms Level 1: monomeric unites Level 2: Macromolecules Level 3: supramolecular complexes Level 4: the cell and its organlles Lecture 2: Life Chemistry and Energy Concept 2.1 Atomic Structure is the Basis for Life’s Chemistry - Living and Nonliving matter is composed of atoms. - Like charges repel; different charges attract. - Most atoms are neural because the number of electrons equals the number of protons. o Neutrons do not carry any charge, protons positive, electrons are negative? - Dalton – Mass of one proton or neutron o (1.7 * 10^ -24 grams) o Measured atoms mass in molecules – mass spectrometer. - Mass of electrons is so tiny (1/2000 of a proton/neutrons), it is usually ignored. - Element o Pure substance that contains only one kind of atom. - Living things are mostly composed of 6 elements: o Carbon (C) o Hydrogen (H) o Nitrogen (N) o Oxygen (O) o Phosphorus (P) o Sulfur (S) - The number of protons identifies an element. - Atomic number o Number of protons - For electrical neutrality, # protons = # electrons - Mass number o Total number of protons + Neutrons o Protons and neutrons do not always equal each other, when they don’t they are called isotopes? - Behavior of electrons determines whether a chemical bond will form and what shape the bond will have. Outside of nucleus. - First shell o 2 electrons maximum o Hydrogen – 1 - Second shell o 8 electrons maximum o Carbon- 6 o Nitrogen – 7 o Oxygen – 8 - Third shell o 18 Electrons Maximum o Phosphorus – 15 o Sulfur – 16 - Atoms with unfilled outer shells (they are not happy) tend to undergo chemical reactions to fill their outer shells. (ex: interacting with other people to get what you need or just taking it) - They can attain stability by sharing electrons with other atoms or by losing or gaining electrons - The atoms are then bonded together into molecules. Concept 2.2 Atoms Interact and Form Molecules - Octet Rule o Atoms with at least two electron shells form stables molecules so they have eight electrons in their outermost shells. - A chemical bond is an attractive force that links atoms together to form molecules. o Because the atom is unstable they do this. - There are several kinds of chemical bonds. - - Ionic bonds - Ions o Are charged particle that form when an atom gains or loses one or more electrons. - Cations o Positively charged ions - Anions o Negatively charged ions - Ionic bonds o Result from the electrical attraction between ions with opposite charges o The resulting molecules are called salts. - Ionic attractions are weak, so salts dissolve easily in water. - Covalent bonds - Covalent bonds o Form when two atoms share pairs of electrons. - The atoms attain stability by having full outer shells. - Each atom contributes one member of the electron pair. - Carbon atoms have four electrons in the outer shell- they can form covalent bonds with four other atoms. - Atoms can share equally or unequally - Electronegivity- - Properties of molecules are influenced by characteristics of the covalent bonds: o Orientation o Strength and stability o Multiple bonds o Degree of sharing electrons. - Orientation o Length, angle, and direction of bonds between and two elements are always the same. o Example:  Methane always forms a tetrahedron. - Strength and stability o Covalent bonds are very strong; it takes a lot of energy to break them. - Multiple bonds o Single – sharing 1 pair of electrons C – H o Double – sharing 2 pairs of electrons C- _ C o Triple – sharing 3 pairs of electrons N- - - N - Degree of sharing electrons is not always equal. o Electronegativity  The attractive force that an atomic nucleus exert on electrons o It depends on the number of protons and the distance between the nucleus and electrons. - If two atoms have similar electronegativity’s, they share electrons equally, in what is called a nonpolar covalent bond - If atoms have different electronegative, electrons tend to be near the most attractive atom, in what is called a polar covalent bond. - Hydrogen bonds - Attraction between the ___ negative end of one molecule and the _____ positive hydrogen end of another molecule forms Hydrogen Bonds. o They form between water molecules o They are important in the structure of DNA and proteins. - Water molecules form multiple hydrogen bonds with each other – this contributes to high heat capacity. o A lot of heat is required to raise the temperature of water – the heat energy breaks the hydrogen bonds. o In organisms, presence of water shields them from fluctuations in environmental temperature. - Water has a high heat of vaporization – a lot of heat is required to change water from liquid to gaseous state. - Thus, evaporation has a cooling effect on the environment. - Sweating cools the body – as sweat evaporates form the skin, heat from the adjacent body is used to transform the sweat from liquid to gas. - Hydrogen bonds also give water cohesive strength, or - Cohesion – o Water molecules resist coming apart when placed under tension. - This permits narrow columns of water to move from roots to leaves of plants. - Hydrophilic (water – loving) - in aqueous solutions, polar molecules become separated and surrounded by water molecules. o Ex: salt and sugar. - Nonpolar molecules are called Hydrophobic (water- hating); o Ex: oil - The interactions between them are hydrophobic interactions. - Functional Groups (important) o Small groups of atoms with specific chemical properties. - Functional groups confer these properties to larger molecules, e.g., polarity. - KNOW: FIGURE 2.7: functional groups important to living systems. Part one and Part two&3 - One biological molecule may contain many functional groups. Lecture 3: Concept 2.2 Atom Interact and form Molecules 1/ 11/ 2016 - Macromolecules o Are large molecules formed by covalent linkages of smaller molecules. - 4 kinds of macromolecules are typically found in living organisms. o Proteins o Nucleic acids o Carbohydrates o Lipids - Except for the lipids, the other 3 kinds of Biological Macromolecules are Polymers (“poly” = many; “mer” =unit). - Polymers are created by the covalent linkage of smaller molecules called Monomers. - Polymers are formed and broken apart in reactions involving water. - Condensation o The removal of water creates a covalent band between monomers. - Hydrolysis o The addition of water breaks a covalent bond between monomers. - Two major energy source: carbohydrates and lipids. - Endergoninc- anabolic reaction - Exergoninc- catabolic reaction. Concept 2.3 Carbohydrates consist of sugar Molecules - Carbohydrates are a large group of molecules that have similar composition, but differ in several important properties. - Carbon never bonds with water. o Composition: (Cn(H2O)n’ - Some carbohydrates are small and are called simple sugars. - Some carbohydrates are large and are polymers of the simple sugars. - Five- Carbon sugars (pentoses) - Ribose (RNA) and deoxyribose(DNA) each have five carbons, but very different chemical properties and biological roles. - Six – Carbon sugars (hexoses) - These hexoses all have the formula C6H12O6, but each has distinct biochemical properties. o MANNOSE o GALACTOSE o GLUCOSE o FRUCTOSE - Glucose and fructose makes sucrose - Monosaccharides are covalently bonded by condensation reactions that form glyosidic linkages. - Sucrose is s disaccharide. (fun fact: average, American consume 100 pounds of sugar and sweeteners each year, or almost 30 teaspoons a day.) - Oligosaccharides o Contain several monosaccharides. o Many have additional functional groups o They are often bonded to proteins and lipids on cell surfaces, where they serve as recognition signals. - Polysaccharides o Are large polymers of monosaccharides; the chains can be branching. o Starches  A family of polysaccharides of glucose, the principal energy storage compound of plants. o Glycogen  Highly branched polymer of glucose; main energy storage molecule in mammals  Can be found in liver. And it is heavily branched than starches. o Cellulose  The most abundant carbon – containing (organic) biological compound on Earth; stable; good structural material, in plant cell wall - Why organisms do not store glucose, but starch or glycogen? o Glucose has very high osmosis pressure.- draw water very extensively. o Starch and glycogen has very low osmotic pressure. Which is very safe. - Cellulose is an un branching polymer of glucose with linkages that are chemically very stable - Glycogen and starch are polymers of glucose with branching of carbon. Concept 2.4: Lipids are Hydrophobic Molecules - Lipids o Are hydrocarbons (composed of C and H); they are insoluble in water because of many nonpolar covalent bonds. o Note: Gas is a Hydrocarbon. - When close together, weak but additive van der Waals interactions hold them together. - Store energy in C – C and C – H bonds. - Play a structural role in cell membranes. - Fat in animal bodies serves as thermal insulation. - Triglycerides (simple lipids). o Fats  Solid at room temperature o Oils  Lipids at room temperature - They have very little polarity and are extremely hydrophobic. - Triglycerides consist of: - Three Fatty Acids o Nonpolar hydrocarbon chain attached to a polar carboxyl group (-- COOH) (carboxylic acid) - One Glycerol o An alcohol with 3 hydroxyl (-- OH) groups. - Synthesis of a triglyceride involves three condensation reactions. - Fatty acid chains can vary in length and structure. - In saturated fatty acids, all bonds between carbon atoms are single; they are saturated with hydrogens. - In unsaturated fatty acids, hydrocarbon chains contain one or more double bonds. These acids cause kinks in the chain and prevent molecules from packing together tightly. o Allow membranes to be more flexible. o Deposit In blood flow and can clog the arteries. (not good for us) - Fatty acids are amphipathic: they have a hydrophilic end and a hydrophobic tail. - Phospholipid o Two fatty acids and a phosphate compound bound to glycerol. - The phosphate group has a negative change, making that part of the molecule hydrophilic. - Head- positive charge- Hydrophilic head, and tail – hydrophobic. - Watch video on macromolecule, carbohydrates, and lipids. Concept 2.5 : Biochemical Changes Involve Energy - Chemical reactions occur when atoms have enough energy to combine, or change, bonding partners. o Involves energy. - Sucrose + H2O  Glucose + Fructose - C12h22o11 (C6H12O6) (C6H12O6) - Reactants Products - There are two basic types of energy: - All forms of energy can be considered as either: o Potential:  The energy of state or position, or stored energy  Starch and glycogen, stolen energy, o Kinetic  The energy of movement (the type of energy that does work) that makes things change. - Energy can be converted from one form to another. - There are two basic types of metabolism: - Anabolic reactions: Link simple molecules to form complex ones. o They require energy inputs (endergonic or endo thermic) o Energy is captured in the chemical bonds that form. - Catabolic reactions: energy is released (exergonic or exothermic) o complex molecules are broken down into simpler ones o Energy stored in the chemical bonds is released. - The laws of thermodynamics apply to all matter and energy transformations in the universe. o First law: Energy is neither created nor destroyed. o Second law: disorder (entropy) tends to increase. - When energy is converted from one form to another, some of that energy becomes unavailable for doing work. - Metabolism creates more disorder (more energy is lost to entropy) than the amount or order that is stored. - Example: o The anabolic reactions needed to construct 1 kg of animal body require catabolism of about 10 kg of food. - Life requires a constant input of energy to maintain order. Nucleic Acids, Proteins, and Enzymes 01/13/2016 Concept 3.1 Nucleic Acids Are Informational Macromolecules - Nucleic acids o Are polymers specialized for storage, transmission, and use of genetic information. - DNA = deoxyribonucleic acid - ATCG - RNA = ribonucleic acid - AUCG - Monomers: Nucleotides (building blocks) - Amino acid make bnds through condenstation - DNA contains deoxyribose - RNA contains ribose - Nucleotides bond in condensation reactions to form phosphodiester linkages. - Nucleic acids grow in the 5’ (5 carbon attached to phosphate) to 3’(three carbon OH) direction. - - Oligonucleotides o have about 20 monomers, and include small RNA molecules important for DNA replication and gene expression. - DNA and RNA are polynucleotides, the longest polymers in the living world. - - Memorize : table 3.1 Distinguising RNA FROM DNA. - DNA- Sugar (deoxyribose) – Base Pyrlmidliners (Cytosine and Thymine) – Base Purines (Adenine and Guanine) – Stand double. - RNA – sugar (Ribose) – Base Pyrlmidliners (Cytosine and Urcil) – Base purines (Adnine and Guanine) – Strands (Single). - - Complementary base pairing: o Adenine and thymine always pair (A-T) (double bonds) o Cytosine and guanine always pair (C-G) (triple carbon bond) - - Base pairs are linked by hydrogen bonds. - There are so many hydrogen bonds in DNA and RNA that they form a farily strong attraction, but not as strong as covalent bonds. - Thus, base pairs can be separated with only a small amount of energy. - - Top hat question: o Which of the following amino acid is basic? Lysine— - - RNA is usually single – stranded, but may be folded into 3-D structures, by hydrogen bonding. - Folding occurs by complementary base pairing, so structure is determined the order of bases. - - DNA – two polynucleotide strands form a “ladder” that twist into a double helix. - Sugar – phosphate groups form the sides of the ladder (on the outside), the hydrogen bases form the rungs (on the inside). Turn is always an right hand turn. - “central dogma” - DNA (transcription) RNA(Translation) Polypeptide (this is what we call “central dogma”). - Dna is an informational molecule: genetic information is the sequence of base pairs. - DNA has two functions: - Replication - Gene expression – o base sequences are copied to RNA, and specify amino acids sequences in proteins. - - DNA replication and transcription depend on the base pairing. - - DNA replication and transcription depend on the base pairing: - 5’- T C A G C A – 3’ – Coding strand - / / / / / / - 3’- A G T C G T – 5’ – Template strand - (polymer chain reaction) - 3’ – AGTCGT- 5’ transcribes to RNA with the sequence 5’- UCAGCA-3’ - Template strand – transcribe into Rna. - - Genome- o complete set of DNA in a living organism o Genomics- study of the genome - Genes – o DNA sequences that encode specific proteins and are transcribed into RNA and translated to specific protiens. o Gd o fdf - Not all genes are transcribed and translated in all cells of an organism. - - DNA base sequences reveal evolutionary relationships. - Closely related living species should have more similar base sequences than species that are more distantly related. - Scientists are now able to determine and compare entire genomes of organisms to study evolutionary relationships. - - Major functions of proteins: - Enzymes – o catalytic proteins o Allow us to digest food. - Defensive proteins (e.g., antibodies) o The reason that we can sense the environment. - Hormonal and regulatory proteins – o control physiological processes - Receptor proteins – o Receive and respond to molecular signals. - Storage proteins store amino acids. - Structural proteins – o physical stability and movement - Transport proteins carry substances (e.g., hemoglobin) - Genetic regulatory proteins regulate hen, how and to what extent a gene is expressed. - - Protein monomers are amino acids (building block of protiens. - Amino and carboxylic acid functional groups allow them to act as both acid and bas. - The R Groups differs in each amino acid. GO OVER PROTIENS WATCH VIDEOS! - Amino acids with electrically charge hydrophilic side chains. - Amino acids with polar, uncharged, hydrophilic side chains. - Amino acids with nonpolar, hydrophobic side chains. - Cysteine side chains can form covalent bonds with other cysteine side chains. – disulfide bonds - This type of S ---- S bond is called a disulfide bridge, or a disulfide bond. - TAKE NOTES FROM THE CHARTS/ TABLES - Top Hat question: - Nucleotides in rna are connected to one another in the polynucleotide chian by : o They are single chains o Covalent bonds between sugar and phosphate. Chapter three: Nucleic Acids, Proteins, and Enzymes January 15, 2016 Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles. - Additional terms to know: - Oligopeptides or peptides – short polymers of 20 or fewer amino acids (some hormones and signaling molecules.) - Polypeptides or proteins range in size from insulin, which has 51 amino acids, to huge molecules such as the muscle protein titin, with 34,350 amino acids. - Amino acids are linked in condensation reaction s to form peptide linkages or bonds. - Polymerization takes place in the amino to carboxyl direction. – covalent bond - Figure 3.6 Formation of a Peptide Linkage. - There are four levels of protein structure: o Primary o Secondary o Tertiary o Quaternary - Primary structure o is a single chain - Secondary structure o Regular, repeated spatial patterns in different regions, resulting from hydrogen bonding. - There are 2 major types of secondary structure: o a (alpha) helix – right handed coil  back bond hydrogen bonds allow the alpha helix to be form. o b (beta) pleated sheet – two or more polypeptide chains are extended and aligned. - Tertiary Structure: o Is the final, folded, 3-D shape of a polypeptide. o Is determined by interactions between R- groups, rather than between backbone constituents. - Interactions between R groups determine tertiary structure. o Disulfide bridges hold a folded polypeptide together  Big player in 3-d bonds  sh o Hydrogen bonds stabilize folds o Hydrophobic interactions side chains can aggregate  Rings around o Van der Waals interactions between hydrophobic side chains o Ionic interactions from salt bridges.  Positive and negative - Top hat questions - Which of the following interactions in protein tertiary structure is covalent o Disulfide bridges - Which statement about the structure of a protein is true? - Quaternary structure o Two or more polypeptide chains (subunits) bind together by hydrophobic and ionic interactions, and hydrogen bonds. o Very week bonds NO covalent bonds!!! o These week interactions allow small changes that aid in the proteins function. o Protein that care oxygen throughout the body - THERE IS A TABLE I FORGOT TO WRITE HERE. - - Secondary and tertiary protein structure derive from primary structure. - Denaturing- o heat or chemicals are used to disrupt weaker interactions in a protein, destroying secondary and tertiary structure. o All the bonds form 3d bonds and they are disruptive.. - The protein can sometimes return to normal when cooled – all the information needed to specify the unique shape is contained in the primary structure. - - Factors that can disrupt the interactions that determine protein structure (denaturing): o Temperature o Concentration of H o High concentrations of polar substances, e.e., urea o Nonpolar substances, e.g., organic solvent, acetone.  They denature the proteins - - Chemical bonds and interactions - Primary – covalent bonds (peptide bonds) – amino acid sequences - Secondary – Hydrogen bonds – α helix, β pleated sheet - Tertiary – all five bonds and interactions – folded proteins; enzymes - Quanternary – Hydrophobic interactions between subunits; hemoglobin Concept 3.3 Some proteins act as enzymes to speed up biochemical reactions - Living systems depends on reactions that occur spontaneously, but without help at such slow rates that organisms could not survive. - Catalysts are substances that speed up reactions without being permanently altered. - No catalyst makes a reaction occur that cannot otherwise occur. - Most biological catalysis are proteins (enzymes); a few are RNA molecules (ribozymes). - - In exergonic reactions there is an energy barrier between reactions and products. - An input of energy (the activation energy of E) will put reactants into a transition state. - “not spontaneous due to energy barrier” - - Enzymes lower the activation energy – they allow reactants to come together and react more easily. - Example: A molecule of sucrose in solution may hydrolyze in hundreds of years; with sucrose present, the same reaction occurs in 1 second! - ;n - Enzymes are highly specific – each one catalyzes only one chemical reaction. - Reactants are substrates; they bind to a specific site on the enzyme – the active site. - Specificity results from the exact 3-D shape chemical properties of the active site. - The Enzyme- Substrate Complex (ES) is held together by hydrogen bonding, electrical attraction, or temporary covalent bonding. - E + S <--> ES <-> EP <-> E + P - The enzyme is not changed at the end of the reaction.


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