BSC2010 Week 1 and Week 2 Lecture Notes
BSC2010 Week 1 and Week 2 Lecture Notes
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Date Created: 01/12/16
BSC 2010 Lecture Notes Sixue Chen Week 1 Chapter 1: Principles of Life Science is based on quantifiable observations and experiments o Observation is enhanced by technology: microscopes, imaging, genome sequencing, satellites o Observations must be quantified my mathematical measurements o Inductive reasoning allows one to make general conclusions based on a limit set of observatons o These general conclusions allow the scientist to predict that the same results will be obtained in the future under similar circumstances Example: Sun rises in east, sets in west, predict that sun will rise in east and set in west. Question: why does the sun rise in the east and set in the west? Hypothesis: earth is rotating relative to the sun Experiment: pendulum to try and observe the effects of the earth rotating o Deductive reasoning: Scientific method (hypothesis-prediction method (H-P)) o Observations o Questions o Hypotheses o Predictions o Tests of the predictions (experiments) Role of hypothesis in inquiry o Observation: flashlight doesn’t work o Question: why doesn’t it work? Hypothesis 1: batteries are dead Hypothesis 2: bulb is burnt out o Then test the hypotheses Closer look a hypotheses o Must be testable and falsifiable o Hypothesis-based science often makes use of two or more alternative hypotheses o Failure to falsify a hypo does not necessarily prove that hypothesis Limitations of science o Observations and experiments must be repeatable o Science cannot support or falsify supernatural explanation, because they are outside the bounds of science Chapter 2: Life Energy and Chemistry Atomic Structure is the Basis for Life’s Chemistry o Living and nonliving matter is composed of atoms Nucleus Protons (+) Neutrons (neutral) o **Protons not equal not # neutrons like charges repel; different charges attract most atoms are neutral bc number of electrons equals the number of protons Dalton – mass of one proton or neutron (1.7x10^-24) Electrons th o So tiny (1/2000 of proton/neutron) How do we measure atoms/molecules? Mass spectrometer It will change your life o Element: pure substance that contains only one kind of atom Livin things are mostly composed of CHNOPS Number of protons identifies an element Atomic number = number of protons For electrical neutrality, # protons = # electrons Mass number = total number of protons + neutrons Behavior of electrons determines whether a chemical bond will form and what shape the bond will have Isotopes are variants of an element with additional neutrons in the nucleus o Bohr Model First shell: 2e Second shell: 8e Third shell: 18e **carbon atomic mass = 12, not 6, atomic number = 6 Atoms with unfilled outer shells tend to undergo chemical rxns to fill their outer shells The atoms are then bonded together into molecules Atom with 7 protons and 7 protons has an atomic mass of 14 o Octet rule Atoms with at least two electron shells form stable molecules so they have eight electrons in their outermost shells A chemical bond is an attractive force that links atoms together to form molecules Sodium has 1e in outer shell, so gives it away instead of gaining 7e Chemical bond: attractive force bw atoms, share/donate/gain electrons There are several kinds of chemical bonds; Ionic o Bond energy = 3-7, weaker o Ability of an atom to attract electrons = electronegativity High = has more electrons so attracts what it needs Low = has small amount of electrons so gives it away o Ionic bonds can be broken down in water, when the solvent dissolves can be broken down o Link an atom that donates electrons to an atom that gains the donated electrons Covalent o Bond energy = 50-110 (super strong) o When two atoms share electrons o 2 H atoms share their atoms, so they both have 2 in their shell o same for oxygen atoms o carbon = most versatile bc only has 4e in outer shell ex: methane (CH4) o N2 (nitrogen gas) bonded by triple bonds o Can be shared equally or unequally o Polarity: oxygen draws electrons towards itself, becomes slightly negative (unequal), also look at electronegativities Methane = nonpolar covalent, all equally bonded o may contain electrons shared unequally bw nuclei o can be polar or nonpolar Hydrogen o Bond energy = 3-7 o Sharing of a H atom hydrophobic Van der waals o Water Water molecules form multiple hydrogen bonds with each other – this contributes to high heat capacity A lot oof heat is required to raise the temperature of water – the heat energy breaks the hydrogen bonds In organisms, presence of water shields them from fluctuations in environmental temperature Water has high heat of vaporization - a lot of heat is required to change water form liquid to gaseous state evaporation cools off our environment sweating cools off the body, sweat evaporates from skin, heat form adjacent body is used to transform sweat from liquid to gas hydrogen bonds also give water cohesive strength or cohesion water molecules resist coming apart when placed under tension permits narrow columns of water to move from roots to leaves of plants water is a live solvent, makes life possible Hydrophillic “water loving” – in aqueous solutions, polar molecules become separated and surrounded by water molcules Ex: carboxyl group (carboxylic acid, acidic acid [vinegar]), glucose (sugar dissolves easily in water) Hydrophobic “water hating”: nonpolar molecules, Have a lot of carbon chains Ex: oil o Functional Groups Small groups of atoms with specific chemical properties Functional groups confer these properties to larger molecules, eg polarity One biological molecule may contain many functional groups Sulfhydryl By giving up H, two SH groups can react to form disulfide bridge Functional Groups Hydroxyl In ethanol (alcohols) OH Polar, hydrogen bonds with water to help dissolve molecules. Enables linkage to other molecules by condensation Aldehyde In acetaldehyde (aldehydes) C=O group is very reactive, important in building molecules and in energy- releasing reactions Keto In acetone (ketones) o Important in carbohydrates Carboxyl In acetate (carboxylic acids) Acidic, ionizes in living tissues COOH Amine Amino Can attract H+ ion Phosphate Phosphate Negatively charged Found in DNA molecule Sulfahydryl By giving up H, two SH groups can react to form disulfide bridge Week 2 1/11/16 Atoms interact and form molecules o Macromolecules: large molecules formed by covalent linkages of smaller molecules 4 kinds of macromolecules: proteins nucleic acids carbohydrates lipids Except for lipids, other 3 kinds of biological macromolecules are polymers (“many units”) Created by the covalent linkage of smaller molecules called monomers polymers are formed and broken apart in reactions involvig water o condensation: removal of water creates a covalent bond between monomers o Hydrolysis: additon of water breaks a covalent bond between monomers Condensation o Two monomers come together an lose water, creates polymer (synthesis) o Requires energy, endergonic (anabolic) reaction o Two major energy sources = carbohydrates and lipids Hydrolysis o Like digesting food o Break down polymers into monomers, need to add water to break the bond to create monomers (glucose) o Exergonic (catabolic) reaction, loses energy o Carbohydrates Consist of sugar molecules Carbohydrate – large group of molecules that have similar composition, but differ in properties Composition (CnH2O)n’ = carbo-hydrate Some carbos are small (simple sugars) Large: polymers of the simple sugars **serve as recognition or signaling molecules Five carbon sugars (pentoses) Ribose and deoxyribose each have five carbons o Ribose: extra OH, o Deoxyribose: extra H Six carbon sugars (hexoses) Mannose galactose glucose fructose Simple sugars Monosaccharides are covalently bonded by condensation reactions hat form glycosidic linkages Sucrose is a disaccharide (glucose + fructose) Polysaccharides are large polymers of monosaccharides; the chains can be branching Starches: family of polyaccharides of glucose, principal energy storage compound of plants; can be branched Glycogen: highly branched polymer of glucose; main energy storage molecule in mammals (muscles,etc) Cellulose: most abundant carbon-containing (organic) biological compound on Earth; stable; good structural material, in plant cell wall. Glycogen vs starch: glycogen = highly branched, starch = moderately branched **starch does not have parallel strands Why don’t organisms store glucose, but starch or glycogen? o Glucose takes a lot of water from the cells, glucose has high osmotic pressure so it will draw a lot of water from the cells **know molecular structure of cellulose and starch and glycogen branching: 1-6 linkages between starch and glycogen o 1-4 between sugars themselves monosaccharides are joined together by glycosidic linkages breakdown of carbohydrates could be linked to anabolism of lipids o lipids are hydrophobic molecules lipids are hydrocarbons (composed of C and H); they are insoluble in water bc of many nonpolar covalent bonds 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 fats: solid at room temperature oils: liquid at room temperature Have little polarity and are extremely hydrophobic Triglycerides consist of: o 3 fatty acids (nonpolar hydrocarbon chain attached to a polar carboxyl group (-COOH) (carboxylic acid)) fully saturated = saturated with carbon = not flexible monounsaturated fatty acid (oleic acid/linoleic acid) consist of double bonds more flexible, healthier o 1 glycerol (alcohol with 3 hydroxyl (-OH) groups) backbone of triglyceride o nonpolar and hydrophobic o can contain a mix of saturate/unsaturated/monounsaturated acids synthesis of triglyceride involves three condensation reactions Phospholipids Two fatty acid chains (hydrocarbon) = hydrophobic tail 1 phosphate group = hydrophilic head 1 Choline = hydrophilic head 1 glycerol = hydrophilic head makes the cell more efficient because of the different parts, can carry out different things at the same time. Make up membrane o Energy Potential energy = state of position Kinetic – energy of movement Can be converted from one to another Metabolism creates more disorder, creates more entropy Catabolic Reactions Involve the breakdown of complex molecules into more simple components Synthesis of enzyme lipase would be classified as anabolic bc energy is captured in the bonds linking amino acids that compose lipase Chemical reactions Each chemical rxn involves a change in energyas the atoms in the reactants rearrange to form products o Reactions Exergonic: energy is released to surroundings, bonds formed are stronger than the bonds broken Endergonic: energy is absorbed from the surroundings, bonds being formed are weaker than the bonds being broken Anabolism: building up Catabolism: breaking down 1/13/16 Review: Starch: moderately branched Glycogen: heavily branched Lipids: glycerol + fatty acid Triglyceride = glycerol + 3 fatty acid, Saturated = saturated with hydrogen Phospholipid: Charged head with two hydrophobic tail Chapter 3: Nucleic Acids, Proteins, and Enzymes Nucleic Acids are Informational Macromolecules o Nucleic acids: polymers specialized for storage, transmission, and use of genetic information DNA = Deoxyribonucleic acid Contains deoxyribose, not ribose Base o Pyrimidines (single rings) Cytosine Tymine Uracil o Purines (double rings) Adenine Guanine Whole structure = nucleotide Base + sugar = nucleoside RNA = Ribonucleic acid Contains ribose Transcribed 5’-3’ (5’=phosphate group, 3’= 3 carbon) Oligonucleotides: have about 20 monomers, include small RNA molecules important for DNA replication and gene expression Polynucleotides: longest polymers in the living world (DNA and RNA are polynucleotides) o DNA vs RNA RNA has uracil instead of thymine o Pairing Complementary base pairing Adenine and thymine always pair (A-T) (purine- pyrimidine) o Not as tight because only 2 o Uracil replaces thymine in RNA (U-A) Cytosine and guanine always pair (C-G) (Purine- pyrimidine) o Tighter bond bc 3 hydrogen bond pairing Linked by hydrogen bonds Fairly strong attraction, but not as strong as covalent Uracil forms two hydrogen bonds and pairs with adenine (2 bond purine) o RNA Usually single stranded but may be folded into 3-D structures by hydrogen bonding Folding occurs by complementary base pairing, so structure is determined by the order of bases o Watson, Crick, Wilkins Discovered double helix DNA – two polynucleotide strands form a ladder that twists into a double helix Sugar-phosphate groups form the sides of the ladder, hydrogen bonded bases form the rungs o Central Dogma DNA is an informational molecule: genetic information is in the sequence of base pairs DNA has two functions: Replication Gene expression – base sequences are copied to RNA and specify amino acids sequences in proteins o The way it is expressed is also affected by our environment, o “DNA is not a destination” o DNA replication Dna replication and transcription depend on base pairing DNA replication and transcription depend on the base pairing Transcription o 2 strands o 1 is coding, other is template strand (will be used as a pairing template) o RNA sequence is made from the template strand with the respective base pairs o Get excited about where science is going!!!!!!! Genome: complee set of DNA in a living organism Genomics: study of a genome Each cell has the same genome, but we have cell differentiation due to gene expression. Genes: DNA sequences that are transcribed into RNA and translated to specific proteins Transcriptome and transcriptomics Proteomics and Proteomics But not all genes are transcribed and translated in all cells of an organism Gene expression analysis Microarray/Gene chip Promotes gene differentitation, we can find out what separates a disease gene from a different gene Green dot = very present Yellow dot = no change o DNA Sequencing DNA base sequences reveal evolutionary relationships Closely related living species should have more similar base sequences than species that are more distantly related This proves evolution We are very similar to chimps (98%) Scientists are now able to determine and compare entire genomes of organisms to study evolutionary relationships Proteins are Polymers with Important Structural and Metabolic Roles o Major functions of proteins Enzymes: catalytic proteins Defensive proteins (antibodies) Hormonal and regulatory proteins: control physiological processes Receptor proteins: receive and respond to molecular signals Storage proteins store amino acids Soy beans are good storage proteins Structural proteins: physical stability and movement Donald trump lol Transport proteins carry substances (hemoglobin) Genetic regulatory proteins: regulate when, how, and to what extent a gene is expressed o Protein monomers are amino acids Amino and carboxylic acid functional groups allow them to act as both acid and base R group differs in each amino acid Some side chains are hydrophobic (lipids) Collagen Most abundant mammal protein (skin, bones, teeth) 3 polypeptide chains forms collagen helix each chain contains 3 polypeptides per turn o how do amino acids form the protein? Peptide bonds Proteins are formed by amino acids o Cysteine Side chains can form covalent bonds with other cysteine side chains This type of –S—S- bond is called a disulfide bridge, or bond 1/15/16 Review: RNA building blocks: AUCG Cysteine is the most easily oxidized, forms sulfhydryl bonds Bottom strand = template, top = coding strand Formation of a peptide linkage o Polymerization takes place in the amino to carboxyl direction o Amino acids are linked in condensation reactions to form peptide linkages or bonds = covalent bond o Oligopeptides: short polymers of 20 or fewer amino acids o Polypeptides: 20+ amino acids o Four levels of protein structure: Primary structure Simple chain of amino acids Secondary Structure Regular, repeated spatial patterns in different regions, resulting form hydrogen bonding 2 major types of secondary structure: o alpha helix: right handed coil o beta pleated sheet: two or more polypeptide chains are extended and aligned Tertiary structure Final folded, 3D shape of a polypeptide Determined by interactions between R groups, rather than between backbone constituents o Disulfide bridges: hold a folded polypeptide together o Hydrogen bonds: stabilize folds o Hydrophobic interactions: allow side chains to aggregate Hydrocarbons are hydrophobic (hydrophobic interactions) o Van der waals interactions: occur between hydrophobic side chains o Ionic interactions: form salt bridges Quarternary structure Two or more polypeptide chains bind together by hydrophobic and ionic interactions and hydrogen bonds o These weak interactions allow small changes that allow small changes that aid in the protein’s function Allow enzymes to become more efficient, due to an increased amount of polypeptides Hemoglobin = quarternary structure Denaturing proteins Secondary and tertiary protein structure derive from primary structure Denaturing: heat or chemicals are used to disrupt weaker interactions in a protein, destroying secondary and tertiary structure The protein can sometimes return to normal when cooled Factors that disrupt interactions: o Temperature o Concentration of H+ o High concentrations of polar substances (ex=urea) o Nonpolar substances (alcohol, organic substances, radiation) Some proteins act as enzymes to speed up Biochemical Reactions o Living systems depend on reactions that occur spontaneously, but without help at such slow rates that organisms could not survive o Catalysts are substances that can speed up reactions without being permanently altered No catalyst makes a reaction occur that cannot otherwise occur Most biological catalysts are proteins (enzymes); few are RNA molecules (ribozymes) o Exergonic reactions there is an energy barrier between reactants and products An input of energy (activation energy) will put reactants into a transition state Reactants are substrates o How do enzymes speed up a reaction? Enzymes lower activation energy, which allows reactants to come together and react more easily Bonds break/form faster and easier Example: sucrase hydrolyzes sucrose in 1 second, rather than sucrose taking 100 years to hydrolyze on its own o Enzymes Enzymes are highly specific: each one only catalyzes one chemical reaction Reactants are substrates: they bind to a spexific site on the enzyme (active site) Specificity results from the exact 3D shape and chemical properties of the active site Sucrose + enzyme (sucrose) = hydrolysis o Enzyme-Substrate complex (ES) is held together by hydrogen bonding, electrical attraction, or temporary covalent bonding
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