AP Bio Unit 1: Molecular Structure

Chemical Context of Life (Ch. 2) 

• Difference between element and compound- Element = one atom ex. Carbon, compounds = multiple atoms ex. CO2 

• Properties of subatomic particles- protons (in the nucleus, make up atomic number, positive charge), neutrons (in nucleus of atom, stabilize it, neutral charge), electrons (form bonds, negatively charged)

• Properties and examples of: single, double, nonpolar, polar, covalent, ionic, and hydrogen bonds. (Note: some bonds may be a combination of the previously listed bonds)- nonpolar = electrons evenly shared, usually between same element, symmetrical structure, polar = electrons unevenly shared, usually the elements are far away from each other on periodic table, one element is more electronegative and therefore has a partial negative charge, covalent bonds involve electron sharing, can be single/ double (meaning one pair shared, two pairs shared), ionic = transferred electron, one element is partially positive, one is partially negative, hydrogen bonds = involve H, NOF, weakest when only one, held together by the partial positive and negative charges from polar bonds. SINGLE POLAR COVALENT BONDS ARE WITHIN MOLECULES, HYDROGEN BONDS ARE BETWEEN WATER MOLECULES. 

• Given molecular structures, the ability to classify molecules and bonds as any of the words listed in the above bullet point-ex. Of each: hydrogen: bonds between multiple water molecules, covalent polar: water molecule, covalent nonpolar: Cl-Cl, ionic: Na-, Cl+

• Ability to recognize the number of hydrogen bonds that a molecule can form based on its molecular structure- if there’s an h bonded to a c, that h cannot form hydrogen bond b/c HC is too nonpolar (hydrocarbons), can form with N, O, F, EVEN IF O AND N BONDED WITH C, CAN STILL FORM HYDROGEN BOND 

• Properties of water linked to its chemical structure- 1. Cohesion: water-water, 2. Adhesion- water-polar surface, 3. High heat of vaporization- high boiling point, 4. High specific heat: difficult for water to change temperature in both directions, 5. Densest at 4 degrees celsius: solid isn't the most dense (UNIQUE), moves too slowly at ice, in cold water it can still move a bit ALSO: “LIKE DISSOLVES LIKE.” 

• Recognition of hydrophilic and hydrophobic molecules, and properties of these molecules- hydrophilic = LIKES water, polar, asymmetrical, NOF, hydrophobic = SCARED of water, nonpolar, symmetrical, hydrocarbons (long chains)

• Properties of acids and bases- Acids: pH under 7, donates H+, H3O+ ions, protons (all basically the same thing), negative charge since donated H+, Bases: Accepts H+, protons, pH over 7, create OH- ions, positive charge since accepted H+ 

• pH calculations- pH = -log [H+], 10^-14M (molar) = [OH-][H+], if base is 10 to a negative whole number, the whole number is the pH. Ex. [H+] = 10^-6 → pH = 6 

Carbon and Molecular Diversity of Life (Ch.3)

• List the 4 major groups of polymers, their monomers, and their elements*ASK KOEHLER- Carbs: simple sugars, CHO, Proteins: amino acids, CHON, Nucleic acids: nucleotides (RNA and DNA) CHONP, Lipids: Fatty Acids, CHO

• The ability to recognize the type of polymer (carbohydrate, nucleic acid, etc.) given its structure- HOW TO TELL CARBS AND LIPIDS APART: carbs usually have oxygen spread out, lipids have long nonpolar chains (usually hydrocarbons) the hexagonal structures indicate chains of hydrocarbons 

• Describe the differences between saturated and unsaturated fatty acids*ASK MS KOEHLER- saturated: hydrocarbon chains connected by single bonds only, unsaturated: one or more double bonds 

• Given a hydrocarbon skeleton, the ability to recognize carboxyl and amine functional groups- amine = amino group, NH2, NH3, etc (has to have N), carboxyl group = COOH- bases have an extra amine group, acids have an extra carboxyl group, neutral has one of each to cancel each other out 

• The ability to draw/predict products of dehydration reactions and hydrolysis for various monomers- dehydration = take a water molecule to make monomers to polymers, has to be at least H2O but can be more than that (ex. OH and OH, so one oxygen will be left over), hydrolysis = add a water to make polymer to monomers 

• Given the structure of an amino acid, the ability to classify into groups such as polar, nonpolar, acidic, and basic- structure: amino group, center carbon atom, hydrogen atom, carboxyl group, R group (special functions), to classify, look at R group: nonpolar will usually have lots of hydrocarbons, even if there is an S or whatever if it’s in the middle and there’s lots of hydrocarbons, it’s still nonpolar. Polar: electronegative atom on the end of R group (O or S or N, acidic: negative charge, extra carboxyl group, basic: positive charge, extra amine group

• Descriptions/identifications of the four levels of protein structure- Primary structure: peptide bonds, amine and carboxyl groups involved, 1 polypeptide chain; Secondary structure: hydrogen bonds, amine and carboxyl groups, 1 polypeptide chain (R groups DO NOT interact), 2 structures: alpha helix and beta pleated sheet; Tertiary structure: ionic, hydrogen, disulfide bridge, hydrophobic interactions, R groups involved ON SAME CHAIN, 1 chain; Quaternary structure: ionic, hydrogen, disulfide bridge, hydrophobic interactions, R groups involved on DIFFERENT CHAINS, 1+ chains

Transport in Vascular Plants (Ch. 29.5-29.6)

• The cohesion-tension hypothesis- movement of water in upwards direction against gravity is guided by the attractive forces between the particles of water known as cohesion 

• The methods by which water and minerals are absorbed by the roots and travel upwards to the shoots- water enters through roots, travel up stem, exit through leaves, water and oxygen exit through stomata, CO2 enters

• How stomata regulate transpiration- guard cells regulate; just watered plant = guard cells swollen, stoma is open to let water out, dehydrated plant = shrunken guard cells, closed stoma to store water

• Interpreting and creating graphs with error bars- “I” indicates the error bars, if error bars don’t overlap then data can be considered significantly different, have to calc standard error of the mean: SEM = s/root of n, s = standard deviation, n = sample size/points, graph the mean of each set on each graph, then add/subtract the SEM to get the upper/lower limits which is the “I” 

• Percent change in mass: (Final Mass - Initial Mass) / Initial Mass X 100