BIO

8/19/26 - 1.1


  • Atoms are the building block of molecules

  • Protons (+), electrons (-), neutrons (0)


  • Covalent bonding

  • One way atoms interact

  • Co = sharing

  • Some electron rules for covalent bonding:

    1. Neutral atoms have equal electrons and protons

    2. Electrons live in "shells"

    3. The first shell can hold 2 electrons

    4. The second shell can hold 8 electrons

    5. The first shell must be filled first

    6. Shells like to have their full complement of electrons

    7. An electron can live in the shells of two atoms that are

    covalently bonded

  • Carbons are implied and not shown in a chain or ring where lines join/bend and not already labeled with another element

  • Hydrogens off carbon are often omitted

  • Single, double, and triple covalent bonds are indicated by 1, 2, or 3 lines

  • The base has 5 carbons

  • The sugar has 5 carbons

  • The O- is because it was an OH- but the H left


  • NEED TO MEMORIZE ON TEST! O>N>C=H

  • Electronegativity is how closely a nucleus holds on to its electrons

  • Partial charges

  • Polar hydrophilic heads

  • Non-polar hydrophobic tails

  • The phospholipid bilayer contains heads on the outside and tails on the inside

  • Amphipathic means both hydrophilic and hydrophobic parts


  • Hydrogen bonds are between different molecules

  • Anything that has a hydrogen attached to a nitrogen, oxygen, or flourine

  • Covalent bonds are between the same molecules

  • Molecules are the groups of elements (H2O, CH4, NH3, etc)


8/21/26 - 1.1 and 1.2

  • Full charges are hydrophilic and can interact with the partial charges on water

  • Partial charges are when electrons do not equal protons


  • Covalent bonds take lots of energy to break

  • Non-covalent bonds take a lot less energy to break


  • Non-covalent bonds

    • Hydrogen bonds

    • Hydrophobic interactions

    • Ionic bonds

    • Van der Waals forces - weakest force but keep hydrophobic interactions together

  • Bonds are easy to break so therefore easy to change

  • Dynamics (change) determines structure


  • Nucleic acids

  • Information storage. Primarily DNA

  • Information transfer. Using information to create structure and therefore function. Primarily RNA

  • Imagine DNA as the book / instruction manual for carpentry. RNA is the actual tools

  • Produced by bonding various smaller molecules together in chains

  • Monomers together form a polymer


  • Nucleotides

  • Monomers of nucleic acids are called nucleotides

  • Phosphate group, small pentose sugar, nitrogenous base

  • Count the primes like a clock


  • Deoxyribose vs ribose

  • “Deoxy” means no oxygen


  • Pyrimidines C and T

  • Purines A and G

  • The short name purines is the bigger structure and the pyrimidines are the bigger structure. Reversed

  • Curvy C and G pair. Straight A and T pair

  • U pairs with A for RNA

  • CUT pyrimidines. Like the pentagon was cut off of a purine


  • Nucleic acids are always constructed by adding a new nucleotide to the 3’ end

  • 5’ to 3’

  • Primary structure is just a sequence of nucleotides


  • Ph. Phosphorus side. 5’

  • OH. OH side. 3’


  • Double helix. Secondary structure. Forms hydrogen bonds between the base pairs

  • G and C form 3 hydrogen bonds. Rhyme

  • A and T form 2 hydrogen bonds

  • Hydrogen bonds parallel. Based on charges. Hydrogen bonds with O and N


  • RNA can catalyze chemical reactions like a protein while DNA cannot.

  • RNA has an OH group on the 2′ carbon of its 5-carbon sugar while DNA has a H on the 2′ carbon of its 5-carbon sugar.



8/24/26 - 1.3

  • Functions of proteins

  • Can be antibodies

  • Enzymes/catalysts speeding up reactions

  • Transport moving things across membranes or the body

  • Communication signaling

  • Immune system

  • Structure like hair, collagen, etc

  • Movement like actin and myacin


  • Monomers make up polymers


  • Each amino acid has a central carbon attached to an amino group, carboxyl group, hydrogen, and R group


  • Lots of amino acids but only 20 that are common


  • Green is hydrophobic because composed of mostly CH bonds that are equal in electronegativity

  • Pink has hydrogen bonds because the Ns and Os can hydrogen bond with other molecules

  • Orange and blue have ionic bonds because they have full charges


  • Cysteine is the singular

  • Cystine is the one that forms a disulfide bond (Sistine Chapel fingers connecting)


  • Polypeptide chains

  • The carboxyl group of one amino acid can react with the amino group of another to form a peptide bond

  • New amino acids are always added to the carboxyl end

  • There is no 3’ and 5’ end for proteins. That is DNA

  • Bonds around central carbon can rotate like a wheel so R group can kind of spin around

  • H cannot rotate and is on the opposite side as the O


  • Proteins fold into four structures

  • Primary - long string

  • Secondary - alpha helix (loops) or beta sheet (2 or more rows) held together by hydrogen bonds

  • Tertiary - 3d folded interactions between R groups

  • Quaternary - 2 or more polypeptides often come together to make 1 functional proteins


  • Not required to memorize amino acid names

  • Read/written as N amino group to C carboxyl group

  • All amino acids have a carboxyl group and amino group that are capable of bonding, but not all do bond

  • Beta sheets can be either parallel or anti-parallel

  • The same bonds that determine tertiary also determine quaternary structure

  • All based on how R groups interact with each other, the backbone, and the order of the protein

  • Every higher level of structure builds on the levels below it