BIOL 4843 1st EditionExam # 1 Study GuideMolecular Biology: Chapter 1What is the definition of molecular biology?- the study of the essential cellular macromolecules (such as DNA, protein, etc.) and the biological pathways between them.Who devised the Central Dogma, and what is it?- devised by Crick- theory of information flow based on what they knew at the time.- 3 main molecules: DNA, RNA, and polypeptides.- DNA to RNA is transcription, RNA to protein is translation.- DNA is information storage, RNA is information transfer, proteins are carrying out instructions from DNA information.Name the major three components of the Tree of Life.- bacteria, archae, and eukaryotes.- overall commonalities between different groups, but different details.Chapter 2: DNA: the Repository of Biological InformationWho were some of the key players in understanding DNA and information flow, and what did they demonstrate?Grandfathers of Molecular Biology (1860s)- Gregor Mendel, the biologist: came up with 3 basic laws of inheritance- Mendel looked at physical traits in generations.- Genotype influences phenotype.- Genotype is internally encoded information that is inherited (like a blueprint).- Phenotype is observable characteristics.- Johan Friedrich Miescher, the chemist: discovered DNA (nucleins).- Miescher went after white blood cells and found a molecule with a lot of phosphorus in it. - He called it a nuclein (didn’t know he had just found DNA).Chromosome Theory of Inheritance- Walter Sutton: 1. genes are located on chromosomes. 2. genes come in pairs.- Thomas Hunt Morgan: studied fruit flies and their white eyesDNA is hereditary material- Frederick Griffith: streptococcus pneumoniae in mice. 2 different strains in agar plates: smooth (virulent, killer) and rough (harmless). Smooth have capsule that prevents getting hurt by mouse’s immune system.- Oswald Avery: Griffith+extraction.- Smooth: mouse dies- Rough: mouse lives- Heat-killed smooth: mouse lives- Heat-killed smooth+rough: mouse dies- DNA from killed smooth+rough: mouse diesOne Gene, One Enzyme- Sir Archibald Garrod: studied alkaptonuria (black urine) - mutation that resulted in an enzyme deficiency- Beadle and Tatum: studied bread mold- used x-rays to see if mutations occurred that prevented amino acid production (called auxotrophy)- mutation disrupts metabolic activity- if a gene is altered, an enzyme is changed, therefore metabolic activity will be changed.- this was found to be not exactly true, so other theories came about.One Gene, One Polypeptide?1. Enzyme = 1 polypeptide or more than one polypeptide2. Enzyme =/= protein always, = RNA sometimes3. 1 gene = 1+ polypeptideDNA is a double helix- Franklin, Wilkins: x-ray diffraction to study 3D structure- Watson, Crick: came up with double helix *insight into biological function from structure*mRNA is the only RNA that can be translated (codes for proteins) (DNA transcribed into mRNA translated into proteins).Noncoding or functional RNA: example is found in ribosomes. Includes:- tRNA: adaptor molecule that reads nucleotides in mRNA and carries amino acids.- rRNA: along with protein, rRNA make up ribosomes.RNA is synthesized on template strand by RNAP (RNA polymerase).Translation- Ribosome: 2 subunits, large and small.- rRNA and protein- rRNA and tRNA are much more abundant than mRNA.What can happen if the sequence of DNA changes?- Mutations- Hereditary material: DNA damage, repair systems (damage does not necessarily mean mutation).- Lack of repair followed by replication leads to mutations.- Mutations can be detrimental, neutral, beneficial.- Silent mutations do not alter protein sequence or function.- example: GAG ----> GAA (both code for glutamate so no effect) DNA change, but no amino acid change.- Mutations that alter protein sequence and function can be beneficial or harmful.- example: GAG ----> GTG (glutamate (hydrophilic) to valine (hydrophobic)) DNA change, and amino acid change.- Sickle-cell anemia: 4 subunits, 2 alpha, 2 beta.- beta subunit mutationChapter 3: Chemical Basis of Information MoleculesNucleic acids: what are the building blocks and how do they differ between DNA and RNA?- Nucleic acid monomers: nucleotides- 2’ carbon: H in DNA, OH in RNA- 3’ and 5’ carbons are important in directionality- ACTG DNA deoxyribose sugar- ACUG RNA ribose sugar- Nucleotide is phosphate+sugar+base *Important to know the distinction*- Nucleoside is just sugar+baseNucleotides are joined by phosphodiester bonds (covalent bonds)- built 5’ to 3’- negative charge on phosphodiester backbone.- important: could have a uracil but still be DNA! So look at 2’ carbon to make sure!Structure of DNA molecule- millions of nucleotides long- A and T have 2 H bonds, C and G have 3 bonds (to remember, C G 3 all rhyme)Structure of RNA molecule- shorter than DNA- usually single-stranded so 1 phosphodiester backbone- diversity in shapeChemical modification of nucleotides- methylation (after DNA is replicated)- RNA undergoes methylation and the addition of other functional groups (more varied in modifications than DNA).Proteins: what are the building blocks?1. R group (variable)2. Carboxyl group (C terminus)3. Amino group (N terminus)4. Hydrogen- Goes from N to C terminus (directionality is important).- R group is a unique side chain, varies in charge, size, etc.- Amino acids are joined by peptide bonds - covalent.- Peptide = 2+ amino acid residue- Polypeptide = longer chainProteins have a great diversity of structure and function, for example:a. calmodulinb. dicerc. hemoglobinAll of the above have alpha helices but different functions.Proteins can also be modified post-synthetically.- methylation or phosphorylation, for example.What types of chemical bonds are important in molecular biology?Chemical Bonds and Interactions- covalent bonds (strong): 2 atoms sharing a pair of electrons- ionic bonds: electrons transferred between a metal and a nonmetal, between amino acids in a polypeptide.- single bonds: 2 electrons shared, free rotation on either side of bond.- double bonds: 4 electrons shared, less rotation, more rigidResonance in Bonds- peptide bond has partial double bond characteristicsPolarity in Molecules- water: polar, dipole moment, partial positive, partial negative- methane: nonpolar because it is balancedWeak Chemical Interactions - Van der Waal’s- too far apart = no interaction- too close = repel- need to hit that sweet spot- attractive interactions