BS 161 1st Edition Exam 1 Study Guide Lectures 1 9 Lecture 1 Main themes of cell and molecular biology 1 Matter 2 Energy 3 Organization 4 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 basic Lecture 2 Properties of carbon which contribute to molecular diversity 1 carbon has a valence of four and can form four stable covalent bonds tetrahedron shape 2 chains of differing length can form 3 three types of isomers can form a structural change in structure arrangement of atoms causes change in functionality of molecule b 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 molecule c enantiomers mirror image the asymmetric carbon is bonded to four different atoms 4 branching and ring linked carbon bonds can form Seven main functional groups on hydrocarbon H C molecules 1 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 or more 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 structure 1 Primary the sequence of amino acids in all proteins all proteins have an amino terminal end and a carboxyl terminal end 2 Secondary 3D folding into one of two main types a Alpha helix tight coil b Beta pleated flat flexible sheet 3 Tertiary folding caused by R group interactions disulfide bond formation 4 Quaternary folding caused by polypeptide interactions hydrophobic bonds get buried on the inside hydrophilic bonds come to surface Lecture 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 reactions 2 Structural proteins support something don t move 3 Storage proteins provide a food source for amino acids 4 Transport proteins transiently bind and move something 5 Hormonal protein move from cell to cell and trigger it to regulate some process 6 Receptor protein recognize the hormones and start some response 7 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 antigen 9 Gene expression proteins transcription factors that help ribosome proteins make new proteins Lecture 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 sugar Lecture 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 acids into 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 Energy use and storage Part of the nucleic acid backbone Structure especially in cell walls Often added to make glycoproteins or glycolipids on animal cell surfaces for cellspecific type recognition Chemical structure of monosaccharides Aldose carbonyl