BIOL1500 Test 1 Study Guide PDF

Chapter One: Science and Biology Reasoning and Science Types of Reasoning: ​ Deductive reasoning: applying general laws to understand specific phenomena ​ Inductive reasoning: using many observations to form a conclusion ​ Strong inference: testing and rejecting multiple hypotheses...

Chapter One: Science and Biology Reasoning and Science Types of Reasoning: ​ Deductive reasoning: applying general laws to understand specific phenomena ​ Inductive reasoning: using many observations to form a conclusion ​ Strong inference: testing and rejecting multiple hypotheses ○​ Use of experiments Scientific Method: first developed by Sir Francis Bacon in late 1500s 1.​ Recognition and formulation of a problem 2.​ Collection of data through observation and experiment 3.​ Formulation of hypothesis (best guess at solution for the problem) 4.​ Testing hypothesis in laboratory/controlled conditions Hypothesis versus Theory ​ Hypothesis: a tentative explanation based off of data collected through observation and experimentation ​ Theory: a hypothesis that has survived repeated challenges and has gained a substantial amount of experimental support ​ Law: a statement of an observed phenomena that never changes ​ How does a hypothesis graduate to a theory? ○​ Experimental testing! ​ Questions that CANNOT be addressed by science ○​ Supernatural/religious explanations ○​ Hypotheses must be testable and falsifiable Experimental Design Types of experiments: ​ Manipulative: conditions are purposefully altered for one variable while all other variables are constant ​ Controlled: comparing a group that is being manipulated to a control group that is not manipulated at all ​ Natural: observing events that have already happened ​ Blind: researcher does not know which group has received the treatment ​ Double blind: neither subject or researcher knows who is receiving treatment Hypothesis Testing Null versus alternative hypotheses: ​ Null: there WILL NOT BE an effect ○​ I think of it as Null has an “n” and not has an “n” ​ Alternative: there WILL BE an effect Variables ​ Each study has dependent and independent variables ​ Dependent variables are affected by what happens to the independent variable ○​ “They depend on it” ​ IN A GRAPH: dependent variable is on the Y axis/independent variable is on the X axis ○​ Dependent AKA the effect or response ○​ Independent AKA the cause or predictor Three most important types of graphs 1.​ Bar or column graphs: useful for comparing counts/averages/ summary statistics 2.​ Line graph: used for data that is continuous and has a FIXED ORDER a.​ Ex: time/distance relationships in which points are not independent from each other b.​ Matters what came before and after 3.​ Scatter graph: used for sets of data where dependent and independent variables can be plotted as (X,Y) coordinates thats are independent from each other a.​ The order does not matter b.​ Set up as a Cartesian plane c.​ Dots not connected->input a trendline demonstrating average trend is common d.​ X is usually for cause/Y is usually for effect e.​ If not a casual relationship, Y axis should show the data with more uncertainty Peer reviewed scientific literature ​ Why is this important? ○​ Different types yield different results: original research/ systematic reviews/meta-analyses The process: 1.​ Conduct research ○​ Experiments/comparisons/reports on events/reviews/ meta-analysis 2.​ Analyze data and write paper ○​ Include background information and major conclusions 3.​ Submit to appropriate journal 4.​ Editors evaluate whether paper is a good fit for the journal 5.​ Sent to anonymous reviewers ○​ Other active researchers in field ○​ Look at accuracy/interpretation/soundness of methods/ whether conclusions meet data 6.​ Possible results ○​ Published! ○​ Revise and resubmit ○​ Rejected ): APA Citations Biology: the study of life ​ Homeostasis: regulation of the internal environment to maintain a constant state of equilibrium ○​ Ex: humans sweating to reduce temperature ​ Organization: being structurally composed of one or more cells ○​ Cells are the basic units of life ​ Metabolism: transformation of energy by converting chemicals and energy into cellular components, anabolism, and decomposing organic matter, catabolism ○​ Living things require energy to maintain internal organization (homeostasis) and to produce other phenomena associated with life ​ Growth: maintenance of a higher rate of anabolism than catabolism  ○​ A growing organism increases in size in all of its parts rather than simply just accumulating matter ​ Adaptation: ability to change oliver time in response to the environment ○​ This is fundamental to the process of evolution and is determined by an organism's heredity, diet and external factors ​ Response to stimuli: a response can take many forms and often expressed by movement (ie: leaves of a plant turning towards the sun) ○​ Ex: the contraction of a unicellular organism to external chemicals ​ Reproduction: ability to produce new individual organisms either asexually or sexually ○​ Asexual reproduction: single parent organism, low genetic diversity ○​ Sexual reproduction: two parent organisms, high genetic diversity Functions common to all life: ​ Nutrition ​ Transport/distribution ​ Respiration ​ Excretion ​ Response to the environment ​ Reproduction The Origin of Life ​ All life we know seems to have arisen from a single origin about 4 billion years ago ○​ Evidence: all living things share these characteristics ​ L-isomers of proteins ​ Nuceleic acids (DNA, RNA) ​ Codons ​ Lipid membranes ​ Similarities of basic functional genes ​ Similarities of cellular structure ​ New properties emerge at successive levels of biological organization ○​ Life is studied at different levels- ex:molecules up to the living planet Levels of biological organization: largest to smallest ​ biosphere->ecosystem->community->population->organism->organ-> tissues->cells->molecules->atoms  ​ Emergent properties: result from the arrangements and interaction of parts within a system ○​ Characterize non biological things also ○​ Reductionism: breaking down a complex system to simpler components that are easier to study ​ Ex: molecular structure of DNA helps understand the chemical basis of inheriting traits ○​ Systems biology: combined with reductionism, this analyzes the interactions among the parts of a biological system Molecules: Interactions within organisms ​ Cells are able to coordinate various chemical pathways through feedback ​ Feedback regulation: product of a process regulates said process ​ Positive feedback: self-perpetuating ○​ Amplified sound feedback ○​ Growing trees ○​ Invasive organisms ○​ Ex: childbirth ​ Negative feedback: suppresses change and maintains status quo ○​ Body temperature ○​ Buffered system ○​ Ex: insulin in cells ○​ Most common form of regulations in living organisms!! ​ Response reduces the initial stimulus Evolution: change in frequency of genes in a population ​ Idea that makes logical sense of everything we know about living organisms ​ Scientific explanation for both unity and diversity of organisms is the concept that living organisms are modified descendants of common ancestors ​ INDIVIDUALS DO NOT EVOLVE!! POPULATIONS EVOLVE OVER TIME!! ​ Natural selection: only increase or decrease heritable traits in a population ​ Adaptation: a feature of an organism that has evolved through natural selection ○​ Adaptations vary with the type environment  ​ Other mechanisms of evolution: ○​ Genetic drift (random demographics) ○​ Gene flow (genetic change within a population because of migration) ○​ Sexual selection (effect of mate choice on gene frequencies) ​ After populations have been separated long enough, they can become very different due to accumulating evolutionary changes ○​ The populations become reproductively isolated ○​ This is the actual origin how how new species are formed ○​ Ex: Porkfish populations being isolated by the Isthmus of Panama around 3.5 billion years ago, creating the Panamic Porkfish subpopulation ​ Phylogenetic trees show evolutionary changes over long periods of time through common ancestors ​ Evolution is conservative! ○​ Better to modify an existing part than spend energy creating an entirely new one ​ Evolution accounts for the unity and diversity of all species on Earth Chapter Two: The Chemical Context of Life What is Chemistry? ​ Biology has chemistry at its foundation and subject to the same laws The Basics ​ Organisms are composed of MATTER ​ Matter: anything that takes up space and has mass ○​ Made up of elements ​ Element: substance that cannot be broken down to other substances by a chemical reaction ​ Compound: substance consisting of two or more elements in a fixed ratio ​ Elements in the human body: Oxygen/Carbon/Hydrogen/Nitrogen make up over 96% of body mass (including water) ​ Atoms: smallest unit of matter that retains the properties of an element Three subatomic particles 1.​ Protons (+) 2.​ Neutrons (neutral)  3.​ Electrons (-) ​ Atomic mass: number of protons and neutrons ​ Atomic number: number of protons ​ Number of neutrons= ATOMIC MASS - ATOMIC # ​ Uncharged element: equal number of protons and electrons ​ Isotopes: two atoms of an element that differ in number of neutrons ○​ All atoms of an elements have the same number of protons but may differ in number of neutrons ○​ Radioactive isotopes: decay spontaneously giving off particles and energy ​ Ex: used to determine fossil ages ​ Ex: Carbon14 is used in some medical imaging to detect different diseases Electron Shells and Types of Bonds ​ Electron shells: regions of three dimensional space around the nucleus of an atom where electrons are found ○​ Each shell can only hold a certain number of electrons ○​ Once shell is full, additional electrons will go to the next shell ○​ First shell (innermost): two electrons ○​ Second and ongoing: eight electrons ○​ Last shell (outermost): valence shell ​ If full: atom is nonreactive ​ If not full: will try to gain electrons by sharing or taking them from another atom in order to be full ​ Valence electrons=bonding electrons ​ Ionic bond: involves transfer of electrons from one atom to another so both atoms will have a full valence shell after ○​ Typically formed between a metal and a nonmetal ○​ Now, one atom will be positive and one atom will be negative ○​ Help form and maintain the 3D shapes of proteins->can affect of proteins like enzymes/antibodies function ​ Nonpolar covalent bonds: chemical bond when two atoms share electrons equally because the electronegativity of both atoms is relatively equal ​ Electronegativity: capability of an atom to attract electrons to itself  ○​ An atom with high electronegativity has a stronger electron attraction than an atom with low electronegativity ○​ Ex: when two hydrogen atoms bond together they share electrons equally because they have the same electronegativity ​ Polar covalent bonds: chemical bond that occurs when electrons are not shared equally between two atoms ○​ Atom that is more electronegative has a stronger attraction for electrons=electrons spend more time in the electron cloud of that atom ○​ Unequal sharing of electrons creates a partial negative or positive charge for each atom ​ Higher electronegativity= partial negative charge ○​ Result in charge separation within a molecule but not in a transfer of electrons from one atom to another, and will not result in the formation of ions if the atoms are separated ○​ Ex: HCl->a hydrogen atom and chlorine atom share a pair of electrons but since chlorine is more electronegative, the chlorine atom is partially negatively charged since the shared electrons will spend  more time in that electron cloud. The hydrogen atom will have a partially positive charge ​ Dipole moment: measurement of the charge separation between atoms in a molecule. It is a vector quantity meaning that it has both direction and magnitude ○​ When there is a larger difference in electronegativities the dipole moment is larger ​ Covalent bonds usually involve carbon, oxygen, nitrogen and hydrogen ○​ All are essential for living organisms ○​ These four elements account for 96% of the atoms in our bodies ○​ Sugars such as glucose and fructose which are important sources of energy for living organisms are also held together by covalent bonds ​ Hydrogen bonds: attractive force between a hydrogen atom bonded to an electronegative atom in one molecule and attracted to an electronegative atom in an adjacent molecule ○​ Vital components for DNA: hydrogen bonds hold both strands of the DNA double helix together thus why it is essential hydrogen bonds are easily broken and reformed like unzipping and zipping a zipper in order for DNA to be transcribed ​ Chemical bonds are VERY IMPORTANT for life Chapter Three: Water Properties of Water ​ Polar covalent bond in a water molecule between Oxygen and Hydrogen ​ Can form hydrogen bonds between water molecules which holds them together (because of the slightly negative/positive charged) ​ Hydrogen bonds give water unique properties ○​ Cohesion attraction between two like molecules ○​ Resists change in temperature (EX: coastal climates being cooler) ○​ Expands when frozen (causes lattice structure) ○​ Good Solvent for polar substances Cohesion and Adhesion ​ Hydrogen bonds hold water together ​ Adhesion: water is sticky, attraction between two unlike molecules  ○​ Ex: important in water movement from the roots of a tree up its trunk ​ Cohesion: gives water surface tension ○​ Measure of how difficult it is to stretch or break the surface of a liquid ​ Water resists changes in temperature due to hydrogen bonding ○​ Heat breaks hydrogen bonds, does not cause water to move faster ○​ High heat of vaporization: heat required to get 1g of liquid into a gas Liquid to gas, why so important? ​ Helps maintain constant temperature (EX: evaporative cooling/ homeostasis) Water is a great solvent ​ Hydrophilic: will readily dissolve polar and ionic compounds ​ Hydrophobic: does not like uncharged compounds ​ Water likes charges due to polar covalent bonds Acids, Bases and Salts ​ Acid: a substance which donates a hydrogen ion in solution (H+) ○​ Causes concentration of H+ to increase ○​ EX: citric acid/salicylic acid/sulfuric acid/hydrochloric acid ​ Base: a compound that accepts H+ ○​ Adding a base lowers the amount of H+ in a solution ○​ Functional group: OH ○​ EX: NaOH ​ Salt: form when an acid and a base combine ○​ EX: NaOH + HCl -> Na+ + OH- + Cl- -> NaCl + H2O Measuring pH ​ pH: amount of H+ in a solution ○​ A logarithmic function ​ One unit change is a 10 fold change in the H+ content ○​ Measured on a scale from 0 to 14 ○​ pH=0 means lots of H+ ​ Terminology ○​ Acidic: pH ranges from 0-6.99 ○​ Neutral: pH is 7 (EX: water) ​ Why is water neutral? Equal amount of H+ and OH- ○​ Basic: pH ranges from 7.01-14 Chapter Four: Carbon and the molecular diversity of life Carbon: The Backbone of Life ​ Cells: 70-95% water and the rest is mostly carbon-based compounds ​ Organic chemistry: the study of carbon compounds ○​ Mostly involves CHOPNS (Carbon/Hydrogen/Oxygen/Phosphorus/ Nitrogen/Sulfur) ○​ Creates a diversity of molecules with few elements because of the special properties of carbon ​ Key to an atom’s chemical characteristics is its electron configuration ○​ One carbon can bond to four other atoms ○​ Carbon’s valence shell is half full ​ Typically completes valence shell by sharing electrons in covalent bonds ○​ Single bonds: forms when one electron is shared between two atoms (forms a tetrahedral) ​ Ex: saturated fats are solid at room temperature like butter ○​ Double bonds: forms when two electrons are shared between two atoms (forms a flat molecule) ​ Stronger but shorter ​ Ex: unsaturated fats are liquid at room temperature (olive oil) ​ Hydrocarbons: organic molecules made of only carbon and hydrogen ○​ Nonpolar ○​ Can undergo reactions that release a large amount of energy ○​ Ex: how we are able to drive our cars Sources of Diversity ​ Chain length: number of carbon atoms bonded to each other in a row ○​ Short chain: store less energy ​ Ex: methane ○​ Long chain: store more energy ​ Ex: fats ​ Branching: arranging carbon bonds within a chain above and below also changing the structure of the molecule ○​ 8 carbons can have bonds rearranged in many ways (besides in a row) ○​ If structure changes, function changes ​ Double bonds: prevent molecules from packing tightly together  ○​ ​Cis isomers: molecules where similar atoms or groups are positioned on the same side of a double bond ○​ Trans isomers: same groups as cis isomer but positioned on opposite sides of the double bond ​ Ex: trans fats are harder to break down due to changing the structure of the fat ​ Ring formation: influences molecules shape, stability and function ○​ Ex: sugars, lipids, DNA ○​ Ex: glucose rings are more stable for energy storage Chemical Groups Most Important to Life ​ Functional groups: components of organic molecules that are most commonly involved in chemical reactions ○​ Number and arrangement give each molecule its unique properties Types of groups ​ Hydroxyl group: polar, hydrophilic ○​ makes alcohols soluble in water and influence the chemical reactions ○​ Ex: getting intoxicated from drinking alcohol ​ Carbonyl group: polar, hydrophilic ​ Carboxyl group: polar, hydrophilic ​ Amino group: polar, hydrophilic ​ Sulfhydryl group: nonpolar, hydrophobic ○​ Slightly polar due to electronegativity difference ​ Methyl group: nonpolar, hydrophobic ​ Phosphate group: polar, hydrophilic Chapter Five: Structure and Function of Large Biological Molecules Four types of molecules characteristic to life: ​ Carbohydrates: provide energy and structural support ○​ 1:2:1 ratio of carbon to hydrogen to oxygen ​ Lipids: insulation and building cell membranes ○​ Ex: phospholipids and steroids ○​ Structure: non polar, hydrophobic  ​ Proteins: catalyze chemical reactions, structural, transportation, communication and defense ○​ Ex: enzymes (always end in “-ase”) ○​ Primary, secondary, tertiary and quaternary ​ Nucleic Acids: store and transport information ○​ DNA: genetic instructions ○​ RNA: protein synthesis ○​ Composed of nucleotides, a sugar, a phosphate group and a hydrogenous base Large biological molecules ​ Polymers: long molecules consisting of similar or identical building blocks linked through covalent bonding ○​ Composed of monomers ○​ Ex: starch is a polymer made up of glucose monomers ​ Two reactions ○​ Dehydration reaction: creates polymers ​ “Condensation” reaction ​ Joins two monomers (or a monomer and a polymer) ​ Releases H₂O to form a new bond=creating longer polymer ○​ Hydrolysis reaction: breaks polymers apart ​ “Cleavage” reaction ​ Breaks bonds between units of a polymer ​ Adds H₂O which breaks a bond ​ “Hydro”-water / “lysis”-breaking ○​ These reactions allow us to process the nutrients in food Case of Dementia: CTE and Alzheimer’s Disease Alzheimer’s ​ Primarily affects the elderly ​ Iodine is used to stain brain tissue = noticed large brown regions ​ Substance called Beta-amyloid is a protein that causes for this plaque to form on the brain ○​ Once thought to be called amylose which is a carbohydrate ​ Discovery: mutation in beta-APP is linked to early onset Alzheimer’s disease (they develop symptoms earlier around 51)  ○​ Some mutations involve changes in the amino acid makeup of the beta-APP protein ​ Ex: mutation creating misfolded proteins allow plaques to stick together much better and accumulate on the brain (15% of cases are caused by this mutation) ​ Such as changing amino acid 717 from valine to phenylalanine Carbohydrates ​ Building blocks of energy ​ Sugar molecules- take on various forms depending on bonding and length ○​ Structural ○​ Functional (energy storage) ​ Most abundant macromolecule ​ Monosaccharides (one monomer) ​ Disaccharides (two monomers) ​ Oligosaccharides (between two and ten monomers) ​ Polysaccharides (more than ten monomers) Polysaccharides ​ Complex chains of monosaccharides ​ Storage: energy source for later use ○​ Plants: starch (polymer of glucose) ​ Amylose (unbranched) ​ Amylopectin (branched) ○​ Animals: glycogen (polymer of glucose) ​ Highly branched ​ “Savings account” for energy ​ Structural ○​ Plants (cell wall): cellulose ​ Long unbranched chains of glucose tightly packed together forming fibers ​ Help maintain shape and resist external pressures ○​ Arthropods (insects, spiders, etc): chitin ​ Used for exoskeleton: provides strength and protection Lipids  ​ Diverse group of organic molecules that do not dissolve well in water ​ Nonpolar=hydrophobic ​ Essential for energy storage, membrane structure, and signaling Three broad categories: ​ Fats: energy storage ​ Phospholipids: cell membrane structure ○​ Hydrophilic head ○​ Hydrophobic tails (two) ​ Steroids: class of lipids with distinct four ring structure ○​ Ex: hormones, cholesterol, cortisol Fats (triglycerides) ​ One glycerol and three fatty acid linked together through a dehydration reaction ​ Composed of smaller molecules ○​ Glycerol: three carbon molecule with a hydroxyl group (OH) ○​ Fatty acid: long chains of carbons with hydrogens and a carboxyl group (COOH) attached ​ Saturated = Solid ○​ NO double bonds ○​ Fatty acid chain is relatively straight ○​ Ex: butter (animal fats) ​ Unsaturated = Liquid ○​ Double bonds present (one or more) ○​ Fatty acid chain is kinked ​ Cis double bond causes bending ○​ Ex: olive oil (plant fats) ​ Triglycerides WILL NOT dissolve in water ​ Functions of fats include: ○​ Energy storage ○​ More compact fuel reservoir than carbohydrates ○​ Cushions vital organs in mammals ○​ Insulates against heat loss Phospholipids ​ Contain glycerol linked with two fatty acids and a phosphate group  ​ Makes up major component of cell membranes Steroids ​ Do not contain fatty acids ​ “Characteristic” backbone of four carbon based rings ​ Function as messenger and structural molecules ○​ Hormones: signaling molecules that regulate bodily functions ○​ Cholesterol: crucial component of cell membrane structure to ensure fluidity and stability ​ Travel around and tell different organs different things to do Proteins ​ Have multiple functions in cells (50% of dry mass of a cell) ​ Key roles in: ○​ Structural support: collagen ○​ Transport: transport proteins such as hemoglobin ○​ Chemical messengers: insulin ○​ Antibodies: proteins that fight infections ○​ Enzymes: catalyze reactions ○​ Making hormones: estrogen and testosterone ○​ Producing and using energy: when carbohydrates and fats are unavailable ○​ Energy storage: for later use ​ Made up of 20 different amino acids: “building blocks” ○​ Building proteins is like a game of Scrabble ○​ Determine shape and function of protein ​ Basic structure: amine group, carboxyl group and a side chain ○​ Side chain attached to the 𝛼-Carbon ○​ Change side chain = change properties ​ Peptide bond: amino acids joined together through a dehydration reaction ○​ Polypeptide: a polymer of amino acids which make up proteins Four Levels of Protein Structure ​ Primary structure: a linear chain of amino acids ○​ No specific structure (like beads on a string) ○​ Order of amino acids are critical for final shape ​ Determined by DNA  ○​ No 3D structure yet ​ Secondary structure: due to hydrogen bonds that form between polypeptide backbones (not functional groups) ○​ Two main forms ​ Alpha helix: like a slinky ​ Beta pleated sheets: like an accordion ​ Tertiary structure: generates 3D structure of protein and it is able to function ○​ Interaction between secondary structures within a protein ​ More folded in on itself ​ Results from the interaction between R groups ○​ Bonds include hydrogen bonds, disulfide bonds (like a zip that locks parts of proteins together), ionic bonds and hydrophobic and van der waals interactions ​ Quaternary structure: interaction of two or more proteins coming together ○​ Bonds include hydrogen and disulphide ○​ Ex: hemoglobin Questions from PowerPoint ​ What do lipids, carbohydrates and proteins all have in common? ○​ They all undergo a similar type of reaction linking them covalently into large polymers of repeating monomers. These are linked together by a dehydration reaction.  ​ Why would changing one amino acid cause the whole protein to change shape? ○​ Because they determine how the protein folds, which when changes does not allow proper folding ​ As a potential treatment option, drug developers thought perhaps taking a chemical designed to be more attractive to the basic R-groups on ß-amyloid fragments than the fragments were to each other would prevent their aggregation. Phase III trials of such a drug (Alzhemed) in 2007 failed to show benefits in 1,000 Alzheimer’s patients. What kind of bonds in the ß-amyloid protein was Alzhemed meant to disrupt? ○​ B-Hydrogen Bonds ​ SLIDE 39 in ppt for answers!! You might want to know if you have a mutation in another gene, ApoE4 that changes the amino cysteine to arginine, and affects the age of onset of Alzheimer’s. How could changing the sequence result in a change in function? ○​ B is most correct! All answers accepted except D Nucleic Acids ​ Composed of monomers: nucleotides ​ Phosphate group is important in holding nucleotides together to form that backbone to nucleic acids Two types: ​ DNA (deoxyribonucleic acid) ○​ Encodes your genes (heredity) ○​ Double stranded ○​ Deoxyribose has a hydrogen atom ○​ Two strands (polymers) are antiparallel and intertwine to form a double helix ​ RNA (ribonucleic acid) ○​ An active form of your genes ○​ Functions in protein synthesis ○​ Single stranded ○​ Uracil instead of thymine for its bases ○​ Ribose has a hydroxyl group (OH) ○​ Three type:  ​ mRNA: messenger RNA ​ Carries genetic information from DNA to ribosome ​ tRNA: transfer RNA ​ Brings correct amino acids to ribosome during translation to ensure correct protein is made ​ rRNA: ribosomal RNA ​ Huge part of ribosome which is the structure that synthesizes proteins Nitrogenous bases ​ Pyrimidines: cytosine, thymine, uracil ○​ Single ring ​ Purines: guanine, adenine ○​ Double ring ○​ Larger/more complex structure ​ Pairings: ○​ Cytosine ALWAYS WITH guanine ○​ Adenine and Thymine in DNA ○​ Adenine and Uracil in RNA ○​ Essential for forming double helix in DNA and for functioning of RNA during protein synthesis ​ Complementary strand: a strand of DNA or RNA that is made up of a sequence of bases that match a template strand Polymers of nucleotides ​ Directionality: ’=prime ○​ 5’ carbon end with phosphate group ○​ 3’ carbon end with hydroxyl group ○​ Synthesizing new strand: 5’ to 3’