Molecular Biology - Lecture Notes 1-5

Molecular Biology Exam I Review Sheets Chapter 1: Evolution, Science, and Molecular Biology Molecular Biology: The student of essential cellular macromolecules, including DNA, RNA, and proteins, and the biological pathways that link their biosynthesis How do DNA, RNA, and proteins to one another, and what is the name of the processes which are used to move between these biomolecules? CENTRAL DOGMA (DNA->RNA->Protein) Transcription (DNA->mRNA) & Translation (RNA->Protein) Central Dogma : Which conversions occur via viruses that further changed our understandings of how information flows between DNA, RNA, and protein? Reverse transcription & RNA replication; shows that central dogma is not strictly in the previous order. Which of the above pathways are regulated? All the processes are regulated. What are the requirements of a living system? Requirements: 1. Raw materials - oxygen, hydrogen, carbon, nitrogen, and sulfur (covalent bonds) 2. Energy - derived from the sun, photosynthetic microorganisms collect and store the energy derived from sunlight in chemical bonds 3. Selectively permeable barrier - all cells have phospholipid bilayer, some molecule can diffuse in and out; viruses are different bc they are unicellular 4. Catalysis - reaction allows organisms to sustain life, capacity to accelerate critical molecular processes 5. Biological information - store as DNA, transcribe RNA and then build protein Characteristics (may not need to know): 1. Adaptation 2. Homeostasis 3. Transmission of genetic info between generations 4. Energy acquisition 5. Interactions 6. Growth, development, and death 7. Complexity and organization Heritable changes in an organism genomic information drives: Evolution What events can result in a mutation? Change in a base pair Inversion -- flipped Deletion Insertion What activities can lead to a mutation? DNA replication DNA damage Recombination Transposition - change places What did Miller and Urey prove experimentally and why was this important? Proved that organic compounds could be formed spontaneously by simulating the conditions of Earth's early atmosphere (water, methane, ammonia, hydrogen, nitrogen, and carbon dioxide)  When the Miller and Urey experiment was repeated, and hydrogen cyanide was added as a potential component of Earth’s early atmosphere, what molecule was successfully generated? Adenine What are the lines of evidence that support the idea that the earliest organism may have been RNA based? 1. Catalytic RNAs/Ribozymes 2. RNA can catalyze almost any imaginable reaction needed in a living system 3. RNA is the active component with the capacity to catalyze protein synthesis 4. RNA sequences capable of simple forms of self-replication have been discovered What was on the quiz: 1. Ribosomes use RNA to catalyze protein synthesis 2. RNA can replicate itself 3. There are RNA based viruses What is LUCA and what characteristics did LUCA likely have? LUCA, the last universal common ancestor of all life Characteristics include: ● Simple metabolism ● RNA genetic material ● Primitive ribosome & protein biosynthetic apparatus ● Transcriptional Machinery ● Genetic code What is Charles Darwin credited with? Natural Selection What are the two tenets that must be present for natural selection to occur? Evolution by natural selection is a result of genetic variation within a population and competition between individuals for limited resources Why is the study of evolution linked to molecular biology or in other words, how does molecular biology play a role in evolution? Darwin’s theory of evolution by natural selection has strengthened by modern studies that reveal the sources of genetic variation, mutation, and recombination Understand that while there is a formal scientific method, that many of the great discoveries of our time and those still to come do not necessarily follow this method. The scientific method is malleable, and there are multiple paths to scientific knowledge. All pathways are linked by reliance on reproducible observation or experiment and by their capacity to generate knowledge consistently. *question on quiz → fatty acids in aqueous solution are organized as spherical droplets called micelles Chapter 2: DNA: The Repository of Biological Information What is Gregor Mendel credited with? Founder of modern genetics What plant did he work on with and what led to his success? How was his approach different than his peers? Studied garden peas (Pisum revealed a mathematical pattern in inheritance ; he sativum)  focused on individual traits of plants rather than overall appearance What is Mendel’s first law of heredity? Law of Segregation states that the two alleles for each gene segregate independently into haploid gamete cells What is Mendel’s second law of heredity? Law of Independent Assortment states that alleles for different genes assort into gametes randomly and independent of each other. Understand how to perform a Punnett square and understand the terminology associated with Mendelian genetics. ➢ P generation ➢ F1 generation ➢ F2 generation ➢ Dominant ➢ Recessive How did his work debunk the predominant theory of the time that heredity resulted from a blending of parental traits? Gene Allele Genotype Phenotype What is a gene? An allele? Genotype? Phenotype? Mendel determined that traits sorted independently when he performed two-factor crosses, is this always true? When might this not be the case? No; when two genes for different traits are located on the same chromosome in close proximity to each other, they may not be sorted independently Understand that not every heritable trait follow “Mendelian genetics” Incomplete dominance (red x white = pink) Codominance (red x white = ½ red x ½ white) Linked Genes (chromosomes separate, not genes) What are the stages of the cell cycle? ● Interphase ○ G1 Phase - diploid cell, two copies of everything, one from mom & dad (2n); duplicates cellular content and not chromosomes ○ S Phase - duplicate all information, cell division, highly regulated, four copies instead of two (4n), duplicates all 46 chromosomes ○ G2 Phase - double checks, preparation for mitosis, and fixation of problematic cells, ● M Phase - mitosis, dividing everything into two cells ○ Prophase - condense ○ (Prometaphase) ○ Metaphase - line in center ○ Anaphase - chromatids separate ○ Telophase - nuclear membrane forms ○ (Cytokinesis) - division of parent cell cytoplasm ● (G0 Phase) - non-reproductive phase What is the result of mitosis and how is it different than meiosis? Mitosis - 2 identical diploid cells Meiosis - 4 non-identical haploid cells What is the significance of crossing over and when does this occur? Helps generate diversity within species, the chance of genes on the same chromosome becoming unlinked. Occurs during meiosis. Recombination occurs during prophase 1 of meiosis when a tetrad forms (cross over at chiasmata) What is Thomas Hunt Morgon credited with? What organism did he work with? Drosophila melanogaster , he discovered direct evidence that genes are located on chromosomes from an intense study with fruit flies ● Segregation of white-eye mutant allele w/ x-chromosome ● Suggested genes are associated w/ chromosomes What is the primary exceptional and what is the genetic explanation for these unexpected phenotypes? Primary exceptional - the <0.1% that were white eyed females in Bridges’ fruit fly experiment Genetic explanation is because of nondisjunction of an X chromosome (improper separation of chromosomes during meiosis) ➢ Calvin Bridges' correlation of mutant genes with chromosome abnormalities showed definitely that genes are located on chromosomes. ➢ Linked genes, genes on the same chromosome, violate Mendel’s second law and assort together into gametes. ○ Linked genes must be close together on the chromosome to stay linked ○ The farther apart, the more likely they are separated by recombination during meiosis How did the work of Frederick Griffith and Avery, McLeod and McCarty prove that DNA was the material of heredity? DNA caused bacterial transformation, not proteins. ➢ Transformation of nonvirulent bacteria to virulent bacteria in DNA mice experiment ➢ Griffith showed adding heat-killed virulent bacteria (harmless) to live nonvirulent strain (harmless) permanently transform live strain to lethal, virulent, encapsulated bacteria Griffith believed that the transforming principle was a protein, not DNA ➢ Avery & colleagues extracted DNA from heat-killed virulent pneumococci removing RNA and protein as completely as possible, and added DNA to nonvirulent bacteria, which was permanently transformed into a virulent strain Avery, McLeod, and McCarty determined DNA was the transformation factor Understand the experiment conducted by Beadle and Tatum and what did it prove? ● Experiment raised Neurospora crassa on minimal medium, then transferred to agar with necessary amino acids, then back to simple agar (in which these auxotrophs) no longer grew ● Purposely induced the spores with mutations ● Proved one gene, one enzyme hypothesis ○ Later modified to one gene, one polypeptide  bc some enzyme parts are encoded by different genes How does the information flow, and how have more recent discoveries changed the way we look at the flow of information (i.e. reverse transcriptase) DNA->RNA->Protein Exceptions to viruses: ● ● Reverse transcription (RNA->DNA) RNA Replication in some viruses (RNA->RNA) What are different types of RNA, and do they all become protein? rRNA - combines w/ proteins to form ribosomes, factories for protein synthesis, most abundant tRNA - small adaptor RNA to which amino acids become attached, boomerang shape mRNA - encode proteins and are read by tRNAs to decode a specific amino acid What is functional RNA? Functional RNAs are RNA sequences that are not translated into protein. Rather, the RNA sequences themselves perform functions in the cell. Both rRNA and tRNA are functional RNAs mRNA is translated into protein What are the three possible outcomes of a genetic mutation? And which is a driver of evolution? Harmful Neutral Beneficial Evolution is driven by beneficial mutations What is the significance of a mutation occurring in germ-line cells as opposed to a somatic cell? Mutations that occur in germ-line cells can be inherited ➢ Changes in the DNA sequence of germ-line cells underlie inherited human diseases, cystic fibrosis, and sickle-cell anemia. ➢ Mutations are not always deleterious - can be beneficial and are vital in creating the diversity needed for the evolution of new species Hemophilia is an X-linked recessive disorder, how does this affect the relative likelihood of the male offspring being affected vs. the female offspring? Hemophilia is about 10,000 times more common in females, encoded by the gene on the X-chromosome Understand genetic inherited diseases & general mutations ➢ Hemophilia: internal bleeding, blood does not clot ○ Cause - Point mutation (change in few nucleotides) ■ Sex-linked recessive ➢ Huntington Disease: uncontrollable jerking movements ○ Cause - Insertion ■ Autosomal Dominant ■ Based on # of repetitions of CAG (if you have more than 36 repetitions, then you have a disease) ➢ Sickle Cell Anemia: crescent-shaped blood cells that can’t hold oxygen; resistance to Malaria ○ Cause - Point mutation ■ Autosomal Recessive ■ Cell has valine instead of glutamic acid (hydrophobic vs hydrophilic) which causes the shriveled shape ➢ Cystic Fibrosis: mucus buildup in lungs, chloride ion channels ○ Cause - Deletion ■ Autosomal Recessive, mistake w/ chromosome 7 Chapter 3: Chemical Basis of Information Molecules Understand the structure and function of nucleic acids. What types of bonds are required for nucleic acids to form? The nucleotides of DNA or RNA are linked to chains by phosphodiester bonds What other types of bonds stabilize the DNA double-helix? Hydrogen bonds between complementary base pairs inside helix Van der Waals base-stacking interaction (pi stacking) What is a nucleoTIDE? nucleoSIDE? NucleoTIDE = base + sugar + phosphate NucleoSIDE = base + sugar What is a nucleic acid built from? Polymers of nucleotides; each nucleotide has three components - a deoxyribose sugar (DNA) or ribose pentose sugar (RNA), a phosphate group, and a nitrogenous base (ATCG) How does RNA differ from DNA? Ribose vs. Deoxyribose Uracil vs. Thymine Single-stranded vs. Double-stranded Nucleic acids have directionality, be able to understand and identify a 5’end and a 3’end of a nucleotide. Directionality is defined by the chemical convention for numbering carbon atoms in the nucleotide sugar ring (5’-3’) 5’ carbon has phosphate group attached 3’ carbon has a hydroxyl (-OH) group attached Understand how the sugar component of a nucleotide is numbered. The carbon atoms of a nucleotide sugar molecule are numbered 1’, 2’, 3’, 4’, and 5’ In a nucleotide, the sugar occupies a central position, with the base attached to its 1’ and the phosphate group attached to 5’ What are the different types of nucleotides found in DNA and RNA and how do they associate with each other? Nucleotides have three parts: sugar + phosphate + nitrogen base RNA nucleotides differ from DNA nucleotides by the presence of a hydroxyl group linked to the #2 carbon of the sugar ● Extra hydroxyl group makes RNA polymers less stable than DNA polymers ● More diverse number of shapes compared to DNA Understand the difference between purines and pyrimidines. Purines - two rings ● Adenine ● Guanine Pyrimidines - one ring ● Thymine ● Cytosine What is the structure of an amino acid? a central carbon atom, the alpha carbon atom (a carbon, or C°'), bonded to four different chemical groups. Understand the difference between a ribonucleic acid and a deoxyribonucleic acid. Ribose has one 1 more hydroxyl (-OH) group on the sugar ring than does deoxyribose. ● This OH can become more easily hydrolyzed, making RNA more reactive and less stable than DNA Which has more different types of cellular functions proteins or nucleic acids? Proteins, I think Possible protein sequences = 20^n (n = # of amino acids) Possible DNA/RNA sequences = 4^n (n = # of nucleotides) Understand the structure of polypeptides. Free amino group of the amino acid at one end of the polymer (the amino terminus, or N-terminus) and the free carboxyl group at the other end (the carboxyl terminus, or C-terminus) How does the structure of RNA differ from DNA? ● RNA is typically single strand, DNA is typically double ● Sugars - ribose vs. deoxyribose ● Base - thymine vs. uracil Understand that nucleotides can be further modified. Consider the examples discussed in lecture, why would nucleotides be modified? In DNA, methylation of bases A, C, and G is common and leads to changes in gene expression . In RNA, modifications are more varied and include methylation of bases and/ or ribose and other, more substantial alterations of bases. (inosine can base pair with any nucleotide) What is the monomer used to construct polypeptides? Amino acids , primary structure bonded by peptide bonds Understand that amino acids can be further modified. Consider the examples discussed in lecture, why would amino acids be modified? In each case, the modification alters the behavior of the protein containing the changed amino acid residue. Modifications include the addition of phosphate, sugar, methyl, acetyl, and hydroxyl groups to specific amino acid side chains.