CMB E2 Study Guide 1 PDF

Study guide I 1. What does DNA stand for? DNA stands for Deoxyribonucleic acid. DNA is a polymer and deoxyribonucleotides make up DNA (monomer). 2. What are the building blocks of DNA? The building blocks of DNA are the deoxyribose, nitrogenous base, and a phosphate group. DNA is composed of 4 deoxy...

Study guide I 1. What does DNA stand for? DNA stands for Deoxyribonucleic acid. DNA is a polymer and deoxyribonucleotides make up DNA (monomer). 2. What are the building blocks of DNA? The building blocks of DNA are the deoxyribose, nitrogenous base, and a phosphate group. DNA is composed of 4 deoxyribonucleotides: 1. Deoxyadenosine monophosphate (dAMP) 2. Deoxycytidine monophosphate (dCMP) 3. Deoxyguanosine monophosphate (dGMP) 4. Deoxythymidine monophosphate (dTMP) 3. What makes up the sides of a DNA molecule? The sides of the DNA molecules are made of repeating units of sugar and phosphate molecules. 4. How many base pairs are in a full turn or twist of a DNA molecule? There are 10.5 base pairs per turn. 5. What are the major and minor grooves? The major and minor grooves of DNA are structural features that play a crucial role in the attachment of DNA binding proteins during replication and transcription. Grooves are formed due to the antiparallel arrangement of two backbone strands of DNA. The major groove and the minor groove are distinct and located on the opposite sides of the DNA molecule. The minor grove is formed where the sugar-phosphate backbones are far apart, creating a narrower depression. The major groove is formed where the sugar-phosphate backbones are close together, resulting in a wider depression. 6. Name the enzymes those are involved in DNA replication. The main enzymes involved in DNA replication is: 1. Helicase (unwinds the DNA double helix) 2. Gyrase/Topoisomerase (relieves the buildup of torque while unwinding) 3. Primase (lays down DNA primers) 4. DNA polymerase III (main DNA synthesis enzyme) 5. DNA polymerase I (replaces RNA primers with DNA) 6. Ligase (fills in the gaps) 7. What is the first step that must occur in DNA replication? To begin replication, the double helix must first be opened up and the two strands separated to expose unpaired bases. 8. What enzymes help separate the 2 strands of nucleotides on DNA? DNA helicases uses the energy of ATP hydrolysis to separate the two strands by breaking apart the hydrogen bonds between the bases on the DNA strand. 9. What is the function of DNA polymerase? The function of DNA polymerase: Replication: double the amount of DNA in a cell for cell division and catalyzes the addition of nucleotides to the 3’ end of a growing strand of DNA using a parental DNA strand as a template. Proofreading: proofread the duplicated DNA and self-repair it. 10. How many DNA polymerases are found in E. coli? What are they? What are their functions? There are 3 DNA polymerases found in E. coli. They are DNA polymerase I, II, and III. DNA polymerase III is the MAJOR ENZYME and polymerizing enzyme during chromosome replication. They require a primer-template, and ALL synthesize DNA in the 5’à3’ direction. 11. What are the functions of topoisomerases? How many are they? How they differ? Topoisomerase produces transient nicks in the DNA backbone to relieve tension built up by the unwinding of DNA ahead of DNA helicase. There are two types of topoisomerases: 1. Type I: makes single strand cuts in the DNA. 2. Type II: (dimeric enzymes in eukaryotes) makes double-stranded cuts in the DNA. 12. What is the role of a single strand DNA-binding protein in DNA replication? The role of a single strand DNA-binding protein is that it binds to single-stranded DNA exposed by DNA helicase, preventing base pairs from re-forming before the lagging strand can be replicated. 13. Define a replication fork. A replication fork is a Y-shaped junction at the site where DNA is being replicated. 14. What is Okazaki fragment? What are the average lengths of the Okazaki fragments in prokaryotes and eukaryotes? Okazaki fragments are short length of DNA, including an RNA primer, produced on the lagging strand during DNA replication. Following primer removal, adjacent fragments are rapidly joined together by DNA ligase to form a continuous DNA strand. The average length of okazaki fragments is 100-200 nucleotides long in eukaryotes and between 1000-200 nucleotides long in prokaryotes. 15. What is the direction of DNA synthesis? DNA synthesis is ALWAYS synthesized in the 5’à3’ direction. 16. What Primase does? How are the primers removed at the end of replication? Primase is an RNA polymerase that uses DNA as a template to produce and RNA fragment that serves as a primer for DNA synthesis. Primers are removed by DNA polymerase I and replaced by DNA fragments. 17. What is the proof-reading function of DNA polymerase? Why it is critical for DNA replication? The proof-reading function of DNA polymerase allows the enzyme to check each nucleotide during DNA synthesis and excise mismatched nucleotides in the 3’à5’ direction. 18. What are the differences and similarities of DNA replication in eukaryotes and prokaryotes? 19. What is heterochromatin and euchromatin? Heterochromatin: The region of a chromosome that remains in the form of unusually condensed chromatin. Genepoor. Transcriptionally inactive (silent). Euchromatin: The region of an interphase chromosome that stains diffusely; “normal” chromatin, as opposed to the more condensed heterochromatin. Gene-rich. More easily transcribed. 20. What are nucleosomes? How is it formed? Nucleosomes are beadlike structural units of a eukaryotic chromosome composed of a short length of negatively charged DNA wrapped around a positively charged octameric core of histone proteins; includes a nucleosomal core particle (DNA+ histone protein) along with a segment of linker DNA that ties the core particles together. 21. Define a 30 nm chromatin fiber. Nucleosomes are packed to form a 30-nm fiber. The 30-nm fiber forms a series of loops that pack to form a 300-nm fiber, which in turn coils to form a 700-nm chromatid. 22. What is a histone? A histone is one of a small group of abundant, highly conserved proteins around which DNA wraps to form nucleosomes, structures that represent the most fundamental level of chromatin packaging. 23. Which part of the histone molecule can be modified post-transcriptionally? The N-terminal amino acid tail that extends out from the nucleosome core particle are subject to several types of reversible, covalent modifications that control many aspects of chromatin structure. 24. State the types of modifications. 1. Phosphorylation 2. Acetylation 3. Ubiquitylation 4. Methylation 25. Which amino acid residues are involved in modification? Lysine, Serine and Arginine are involved in modification. 26. How are histone modifications spread on a chromosome? 27. What is histone code? The ‘histone code” hypothesis posits that epigenetic features, specific post-translational modifications act as a unique molecular language to regulate chromatin structure and gene expression. 28. What is epigenetic inheritance? Epigenetic inheritance is inheritance of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA. It can be due to positive feedback loops of transcription regulators or to heritable modifications in chromatin such as DNA methylation or histone modifications. 29. Do prokaryotes have histones? No, most prokaryotes do not have histones except for some members of the domain Archaebacteria (so, the short answer is NO). 30. How many types of histones are in eukaryotes? There are 5 types of histones in eukaryotes: H1, H2A, H2B, H3 and H4. 31. Define the following: ploidy, chromatids, centromere, telomere, replication origin, LTR, transposon, reverse transcriptase. 1. Ploidy: the number of sets of chromosomes in a cell. 2. Chromatids: one of the two identical halves of a chromosome that has been replicated in preparation of cell division. 3. Centromere: the region of the chromosome to which the microtubules of the spindle attach, via the kinetochore during cell division. The centromere also holds the sister chromatids together. 4. Telomere: a region of repetitive DNA sequences (GGGGTTG) at the end of a chromosome. Telomeres protect the ends of chromosomes from becoming frayed or tangled. 5. Replication origin: a nucleotide sequence at which DNA replication is initiated. 6. LTR (long terminal repeat): a polynucleotide sequence found at each end of an integrated retrovirus genome that contains signals for expression of the viral genome. 7. Transposons: a segment of DNA that can move from genome position to another by transposition. 8. Reverse transcriptase: an enzyme first discovered in retroviruses that makes a double-strand DNA copy from a single-strand RNA template molecule. 32. What is telomerase? How it works? What would happen in a cell if it lost telomerase? Telomerase is enzyme that elongates telomere sequences in DNA, which occur at the ends of eukaryotic chromosomes. It is an RNA-dependent DNA polymerase, meaning it is an enzyme that can make DNA using RNA as a template. How it works? The enzyme binds to a special RNA molecule that contains a sequence complementary to the telomeric repeat. It extends (adds nucleotides to) the overhanging strand of the telomere DNA using this complementary as a template in the 5’à3’ direction. When the overhang is long enough, a matching strand can be made by the normal DNA replication machinery (that is, using an RNA primer and DNA polymerase), producing double-stranded DNA. What happens in a cell if it lost telomerase? After many rounds of cell division, telomeres will shrink until they essentially disappear. At this point, these cells will cease dividing. In theory, such a mechanism can provide a safeguard against the controlled proliferation of cells- including abnormal cells that have accumulated mutations that can promote the development of cancer. 33. What are LINES and SINES? Are they really a junk? No, they are not really junk. 34. What is Alu element? The Alu element is a transposable element, known as a “jumping gene.” They are the most abundant repetitive elements in the human genome. 35. What is the function of a chromatin remodeling complex? The chromatin remodeling complex is a multi-subunit protein complex. It possesses a DNA-dependent ATPase activity. It can destabilize histone-DNA interaction in an ATP-dependent manner. It is capable of altering the position of the nucleosomes along DNA.