BS 161 1st EditionFinal Exam Study Guide: Lectures 1-40Lecture 1-Main themes of cell and molecular biology:1. Matter2. Energy3. Organization4. Information-Review from chemistry:-atomic number = number of protons-atomic weight (mass) = protons and neutrons-Types of bonds: the number and type of bond determines the shape and stability of a molecule, as well as its interactions with other molecules-Covalent: strong-Double covalent: very strong-Hydrogen: weak, very abundant, strength in numbers-Van der Waals: very weak, hydrophobic (doesn’t like to be where water is)-Ionic: moderately strong, attraction due to charges (opposites attract)-Chemistry of water: polar molecule (electronegative), polar covalent bonds, good solvent for hydrophobic or charged molecules, makes a hydration shell around proteins and other hydrophilic (water loving) molecules-Hydrophobic: water fearing, nonpolar-Hydrophilic: water loving, polar-some macromolecules are so large that it can have parts that are hydrophobic and hydrophilic-pH: pH = -log[H+]-closer to 0 = acidic-7 = neutral-closer to 14 = basicLecture 2- Properties of carbon which contribute to molecular diversity1. carbon has a valence of four and can form four stable covalent bonds (tetrahedron shape)2. chains of differing length can form3. three types of isomers can forma. structural: change in structure (arrangement) of atoms causes change in functionality of moleculeb. geometric-cis: the two identical atoms are on the same side of the molecule-trans: the two identical atoms are on opposite side of the moleculec. enantiomers: mirror image, the asymmetric carbon is bonded to four different atoms4. branching and ring linked carbon bonds can form-Seven main functional groups on hydrocarbon (H-C) molecules1. Hydroxyl (-OH)2. Carbonyl (C=O)3. Carboxyl (COOH)4. Amino (-NH2)5. Sulfhyrdyl (-SH)6. Phosphate (-PO4)7. Methyl group (CH3)Lecture 3-Proteins: every process uses proteins, important for mutation in evolution, composed of one ormore polypeptide chains held together and functioning as a unit-Protein structure: proteins are unbranched polymers of amino acids, differ in the number and sequence of the twenty types of monomer amino acids-Dehydration (condensation) reaction: removal of a water molecule in order to bond two molecules-Hydrolosis: addition of a water molecule in order to separate two molecules-Peptide: short chain of amino acids-mono = 1-di = 2-tri = 3-oligo = a few-Polypeptide: a single long chain of amino acids (form protein)-Amino acid structure: R groups (also known as side chain, group attached to asymmetric carbon) determine the solubility, shape, and function of protein; amino, carboxyl, and asymmetric carbon are present in all amino acids-Classification and placement of R groups-nonpolar: usually found tucked away from protein surface (hydrophobic)-polar: generally on the protein surface-electrically charged: R group has a second carboxyl or amino group usually on the surface-Organizational levels of protein structure1. Primary: the sequence of amino acids, in all proteins; all proteins have an amino terminal end and a carboxyl terminal end2. Secondary: 3D folding into one of two main typesa. Alpha helix: tight coilb. Beta pleated: flat flexible sheet3. Tertiary: folding caused by R group interactions, disulfide bond formation4. Quaternary: folding caused by polypeptide interactions, hydrophobic bonds get buried on the inside, hydrophilic bonds come to surfaceLecture 4-Proteins differ in life span and location in cells-Protein shape: determined through x-ray crystallography-Chaperonin: chamber that protects protein while it is folding into its shape-Denature: proteins can unfold (denature) artificially, causes loss of function, caused by…-increased temperature-exposure to nonpolar solvents-acids or bases (dramatic change in pH)-Proteins can also lose/gain function naturally by….-regulatory changes: for example adding/taking away a phosphate-mutation: changing the amino acid sequence-Functional classes of proteins:1. Enzymes: catalyze biochemical reactions2. Structural proteins: support something, don’t move3. Storage proteins: provide a food source for amino acids4. Transport proteins: transiently bind and move something5. Hormonal protein: move from cell to cell and trigger it to regulate some process6. Receptor protein: recognize the hormones and start some response7. Contractile and motor proteins: change shape and create movement with help of ATP or GTP (adenine triphosphate or guanine triphosphate)8. Defensive proteins: binds to a particular non-self antigen9. Gene expression proteins: transcription factors that help ribosome proteins make new proteinsLecture 5-Nucleic acid monomers play roles in energy currency, regulation of processes, and making up polynucleotides (DNA and RNA)-Nitrogenous bases: 2 types-Pyrimidines: structure has one carbon ring-cytosine (C): in DNA and RNA-thymine (T): in DNA only-uracil (U): in RNA only-Purines: structure has two carbon rings-Adenine (A): in DNA and RNA-Guanine (G): in DNA and RNA-Nucleotide: base plus deoxyribose sugar plus one to three phosphates-Nucleoside: base plus deoxyribose sugarLecture 6-Sugars (carbohydrates): contain five carbons-deoxyribose: the “de” refers to the lack of oxygen atom in the ribose-ribose-DNA-Structure: double helix shape, antiparallel strands (meaning that the DNA is 5’->3’ on one end and 3’->5’ on the other end), complimentary (meaning that A pairs with T, and G pairs with C)-Replication: DNA is replicated using one strand of DNA as the template for the new strand of DNA-Bonds in DNA-Covalent bonds: found everywhere in the monomer-H-bonds: found between the bases-Phosphodiester bonds: covalent bonds found in the backbone of the DNA strand-Van der Waals bonds: found between the rungs of the ladder of the DNA-RNA-Messenger RNA (mRNA): encode information for amino acids to make proteins-Transfer RNA (tRNA): translate between mRNA and amino acids-Ribosomal RNA (rRNA): about 95% of RNA in a cell is rRNA. These make the amino acidsinto proteins, “protein synthesis machine”-Central Dogma:-Information flows DNA->RNA->protein, cannot flow in reverse order -Transcription: process of information from DNA to RNA-Translation: process of information from RNA to protein Lecture 7-Carbohydrates: the group of compounds including simple sugar monomers (monosaccharides), disaccharides, and macromolecule polysaccharides-Function of carbohydrates: