Term
| Name the 9 advantages of using bacteria & viruses for genetic studies |
|
Definition
1. reproduction is rapid
2. many progeny are produced
3. haploid genome allows all mutations to be expressed directly
4. Asexual reproduction simplifies the isolation of genetically pure strains.
5. growth in the laboratory is easy and requires little space
6. genomes are small
7. techniques are available for isolating & manipulating their genes
8. They have medical importance.
9. They can be genetically engineered to produce substances of commercial value. |
|
|
Term
|
Definition
| plasmids that are capable of freely replicating and able to integrate into bacterial chromosomes |
|
|
Term
|
Definition
| an episome that controls mating and gene exchange in E.coli cells |
|
|
Term
| What are the 3 types of horizontal transfer in bacteria? |
|
Definition
| conjugation, transformation, transduction |
|
|
Term
| How do conjugation, transformation, and transduction differ from eukaryotic sexual reproduction? |
|
Definition
-DNA exchange and reproduction are not coupled in bacteria
-donated genetic material that is not recombined in the host DNA is usually degraded, so the recipient cell remains haploid |
|
|
Term
| What year did Lederberg and Tatum's experiment take place? What was it? |
|
Definition
-1946
-studied auxotrophic strains of E.coli, mixed strains and some turned into prototrophic form, demonstrated that bacteria undergo genetic exchange |
|
|
Term
| What was Bernard Davis's experiment? |
|
Definition
| -but two strains of bacteria in a U-shaped tube with filter in between, no change in auxotrophic bacteria, showed that bacteria must come into contact (conjugate) in order to exchange genetic info |
|
|
Term
| Conjugation can only take place between what cells? |
|
Definition
| cells that possess an F factor and those that do not |
|
|
Term
| What does an F+ and F- cell conjugation result in? |
|
Definition
|
|
Term
| What does an Hfr and F- result in? |
|
Definition
|
|
Term
| Why is there no change between Hfr cell and F- cells? |
|
Definition
| Because in order for an F- cell to become F+ or Hfr, the entire F factor would have to be incorporated, and because it is originally nicked in the middle, this usually doesn't occur |
|
|
Term
| What does F' and F- result in and what is it called? |
|
Definition
| Two F' cells (merozygotes), sexduction |
|
|
Term
| What are E.coli's main advantages as a model organism? |
|
Definition
-fast reproduction
-small size |
|
|
Term
| How many base pairs and how many genes does E.coli have? |
|
Definition
-4.64 million bp
-4300 genes |
|
|
Term
| What is a clear patch of lysed cells called? |
|
Definition
|
|
Term
| What are transducing phages? |
|
Definition
| phage particles that contain bacterial DNA instead of phage DNA |
|
|
Term
| What is intragenic mapping? |
|
Definition
| mapping several mutations within a single gene |
|
|
Term
| What are some examples sicknesses caused by RNA viruses? |
|
Definition
| -common cold, AIDS, influenza |
|
|
Term
| What is HIV and what is AIDS? |
|
Definition
HIV-a retrovirus, Human Immunodeficiency Virus
AIDS-acquired immune deficiency syndrome |
|
|
Term
| Which type of HIV causes most cases of AIDS and what did it come from? |
|
Definition
| HIV-1, comes from SIVcpz in African chimps |
|
|
Term
|
Definition
|
|
Term
| What are the key characteristics of genetic info? |
|
Definition
1. must contain complex information
2. must replicate faithfully
3. must encode the phenotype |
|
|
Term
| What did Miescher discover and what year? |
|
Definition
-1868
-discovered nuclein (DNA) in the nuclei of white blood cells |
|
|
Term
| Who described the nucleus of the cell and what year? |
|
Definition
|
|
Term
| What did Albrect Kossel do and in what year? |
|
Definition
-discovered that DNA contains 4 nitrogenous bases: A, C, G, T
-late 1800s |
|
|
Term
| What did Aaron Levene do and in what year? |
|
Definition
-proposed the tetranucleotide theory (incorrect)
-1910 |
|
|
Term
| What did Erwin Chargaff do and in what year? |
|
Definition
-discovered that there is regularity in the base pairs of DNA (A=T, G=C)
-1948 |
|
|
Term
| Explain Griffith's experiment and state what year it occurred. |
|
Definition
-1928
-mixed heat-killed virulent bacteria with non-virulent bacteria and mice got sick and died
-showed that transformation can occur
-but did not say what the transformation factor was |
|
|
Term
| Describe Avery, MacLeod, and McCarty's experiment and state what year it occurred. |
|
Definition
-1944
-added to Griffith's experiment
-used different enzymes (Protease, RNase, DNase) to destroy parts of DNA to eventually discover that DNA is the transforming substance because DNase destroyed the transforming substance |
|
|
Term
| Describe Hershey and Chase's experiment and state what year it occurred. |
|
Definition
-1952
-tagged phosphorous (DNA) and sulfur (protein coat) with radioactive isotopes
-after centrifugation, discovered that DNA is the genetic material in bacteriophages |
|
|
Term
| What did William Ashbury do and in what year? |
|
Definition
-1947
-used x-ray diffraction to study 3D structure of DNA |
|
|
Term
| What year were Watson and Crick rewarded the Nobel Prize? |
|
Definition
|
|
Term
| In what year did Watson and Crick discover the structure of DNA? |
|
Definition
|
|
Term
| What did Fraenkel-Conrat and Singer do and in what year? |
|
Definition
-1956
-worked with Tobacco Mosaic Virus (TMV) to show that RNA carries genetic material in viruses |
|
|
Term
| Compare and contrast DNA & RNA. |
|
Definition
DNA
-double stranded
-deoxyribose, no oxygen (-H)
-uses thymine
-more stable, less reactive
RNA
-single stranded
-ribose, oxygen (-OH)
-uses uracil
-less stable, more reactive |
|
|
Term
| How do the components of purines and pyrimidines differ? |
|
Definition
-purines are a six sided ring attached to a five sided ring
-pyrimidines are six-sided rings only |
|
|
Term
| What are the 3 components of a nucleotide? |
|
Definition
-a sugar (ribose or deoxyribose)
-nitrogenous base (purine or pyrimidine)
-phosphate group (carries negative charge) |
|
|
Term
| What types of molecular forces hold DNA together? |
|
Definition
-hydrogen bonds
-phosphodiester linkages (covalent) |
|
|
Term
| Name the different types of secondary DNA structures. |
|
Definition
|
|
Term
|
Definition
-most stable and common DNA structure
-occurs when there is plenty of water
-alpha helix
-right-handed (clockwise) spiral
-10 bp per rotation, bp are 0.34nm apart |
|
|
Term
|
Definition
-a structure that exists if there is not enough water present
-shorter and wider
-bases tilted away from main axis |
|
|
Term
|
Definition
-structure of DNA that forms a left-handed (counterclockwise) helix
-results from high salt solution
-sugar-phosphate backbone zig zags back and forth |
|
|
Term
| What is the central dogma of molecular biology? |
|
Definition
proposed by Crick
-says that genetic info passes from DNA to protein in a one-way information pathway |
|
|
Term
|
Definition
the addition of methyl groups to certain positions on the nucleotide bases
-in bacteria, DNA is methylated to distinguish it from foreign DNA from viruses
in eukaryotes, methylation is often related to gene expression |
|
|
Term
| Explain Meselson and Stahl's experiment. |
|
Definition
-used 2 isotopes of N, grew E.coli in a heavy medium and then switched some of them to a light medium
-samples were then centrifuged, and a band of DNA occurred at an intermediate between heavy and light
-supported semiconservative replication (DNA is split and each original strand is used as a template for new DNA) |
|
|
Term
| What were the 3 methods proposed for DNA replication? |
|
Definition
-conservative
-semiconservative
-dispersive |
|
|
Term
| What is the difference between bacterial and eukaryotic replication origins? |
|
Definition
-bacteria only have one
-eukaryotes have many |
|
|
Term
| What are the requirements of replication? |
|
Definition
-template single-stranded DNA
-substrate (raw materials) to be assembled into new nucleotide strand
-enzymes or proteins to help |
|
|
Term
| What begins initiation in bacterial DNA? |
|
Definition
| an initiator protein that binds to the replication origin and causes the beginning of the DNA to unwind |
|
|
Term
| Name the polymerases used in bacterial elongation and describe the function of each. |
|
Definition
-Polymerase I: removes and replaces primers bc of 5' to 3' exonuclease action, has 3'->5' exonuclease action to back up and repair some DNA
-Polymerase II: DNA repair, restarts replication after damaged DNA halts synthesis
-Polymerase III: main workhorse of replication, elongates DNA
-Polymerase IV: DNA repair
-Polymerase V: DNA repair, translesion DNA synthesis |
|
|
Term
| What processes ensure the fidelity of DNA replication? |
|
Definition
-DNA proofreading
-nucleotide selection
-mismatch repair |
|
|
Term
| Name all the components necessary for replication in bacterial cells. |
|
Definition
-initiator protein
-DNA helicase
-Single-stranded binding proteins (SSBs)
-DNA gyrase
-DNA primase
-DNA polymerase III
-DNA polymerase I
-DNA ligase backbone |
|
|
Term
| How does eukaryotic replication differ from bacteria? |
|
Definition
-multiple origins instead of a single origin
-linear chromosomes instead of circular
-DNA is associated with histones, which means nucleosome assembly must occur after replication of DNA |
|
|
Term
| Explain how a cell ensures that replication only occurs once since there are so many different origins of replication in eukaryotes? |
|
Definition
| -DNA uses a licensing factor, which binds to every origin site and once DNA replication machinery initiate replication at these sites, the licensing factor goes away. Replication machinery can ONLY initiate replication on origins that are licensed, so this ensures that it will only occur once |
|
|
Term
| Name the 5 eukaryotic polymerases that we need to know. |
|
Definition
-alpha
-beta
-gamma
-epsilon
-delta |
|
|
Term
| What does alpha polymerase do? |
|
Definition
-initiation of nuclear DNA synthesis and DNA repair
-has primase activity |
|
|
Term
| What does beta polymerase do? |
|
Definition
| -DNA repair and recombination of nuclear DNA |
|
|
Term
| What does gamma polymerase do? |
|
Definition
| -replication and repair of mitochondrial DNA |
|
|
Term
| What does delta polymerase do? |
|
Definition
| -leading and lagging strand synthesis of nuclear DNA, DNA repair, and translesion DNA synthesis |
|
|
Term
| What does epsilon polymerase do? |
|
Definition
| -leading strand synthesis |
|
|
Term
| Describe the role of translesional polymerase. |
|
Definition
-a polymerase with a more active site that can accommodate and copy templates with abnormal bases, distorted structures, and bulky lesions
-can bypass errors but can also cause errors |
|
|
Term
| Name some diseases caused by telomere replication abnormalities. |
|
Definition
-Werner syndrome: early signs of aging
-dyskeratosis congenita:leads to progressive failure of the bone marrow
-can also cause cancer |
|
|
Term
| What is heteroduplex DNA? |
|
Definition
| DNA consisting of 2 strands, each of which is from a different chromosome |
|
|
Term
| Explain the Holliday junction |
|
Definition
| model of homologous recombination that is initiated by single-strand breaks in a DNA molecule |
|
|
Term
| Name all the classes of RNA. |
|
Definition
-mRNA (messenger)
-tRNA (transfer)
-snRNA (small nuclear)
-snRNP (small nuclear ribonucleoproteins)
-snoRNA (small nucleolar)
-scRNA (small cytoplasmic)
-miRNA (micro)
-siRNA (small interfering)
-piRNA (Piwi-interacting) |
|
|
Term
|
Definition
| -makes up the structural and functional components of the ribosome |
|
|
Term
|
Definition
| carries the genetic code for proteins in bacteria and eukaryotes |
|
|
Term
|
Definition
| -helps incorporate amino acids into the polypeptide chain |
|
|
Term
|
Definition
| -processes pre-mRNA in eukaryotes |
|
|
Term
|
Definition
| -processes and assembles rRNA in eukaryotes |
|
|
Term
| What 3 major components does transcription require? |
|
Definition
-DNA template
-substrate
-transcription apparatus (enzymes and proteins) |
|
|
Term
| Who did an experiment to determine that RNA only replicates from one DNA strand and in what year? |
|
Definition
|
|
Term
| What are the components of a transcription unit? |
|
Definition
-promoter
-RNA-coding sequence
-terminator |
|
|
Term
| What is RNA transcribed from? |
|
Definition
| -ribonucleoside triphosphates (rNTPs) |
|
|
Term
| What are the 5 components of bacterial polymerase? |
|
Definition
| -2 alpha, 1 beta, 1 beta prime, and 1 omega(not essential for transcription but stabilizes the enzyme) |
|
|
Term
| What does the sigma factor of RNA polymerase do? |
|
Definition
| controls the binding of RNA polymerase ot the promoter |
|
|
Term
| How many RNA polymerases are there in eukaryotes? |
|
Definition
| 4 (pol I, pol II, pol III, & pol IV) |
|
|
Term
| What does eukaryotic polymerase I do? |
|
Definition
|
|
Term
| What does eukaryotic RNA polymerase II do? |
|
Definition
-transcribes pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs
-is the most important RNA polymerase |
|
|
Term
| What does eukaryotic RNA polymerase III do? |
|
Definition
| -transcribes small RNA molecules: tRNAs, small rRNA, some miRNAs and some snRNAs |
|
|
Term
| What does eukaryotic polymerase IV do? |
|
Definition
| -synthesizes some siRNAs in plants |
|
|
Term
|
Definition
| DNA sequences that are recognized by the transcription apparatus and are required for transcription to take place |
|
|
Term
| What are consensus sequences? |
|
Definition
-sequences that possess considerable similarity
-usually indicate that the sequence is associated with an important function
-found in promotor regions |
|
|
Term
| What are the 3 most common bacterial consensus sequences? |
|
Definition
1. Pribnow box
-5' TATAAT 3'
-located 10bp upstream from start site in the promotor
2. 35 consensus sequence
-TTGACA
-located 35 bp upstream from start site in the promotor
3. upstream element
-contains a number of A-T pairs
-located about 40-60 bp upstream from start site in the promotor region |
|
|
Term
| What are the terminators in bacterial transcription? |
|
Definition
-Rho dependent terminators-uses an Rho protein to help termination
-Rho independent terminator-terminates after a hairpin inverted repeat and then a string of U's |
|
|
Term
| What is polycistronic RNA? |
|
Definition
| RNA that is produced when a single terminator is present at the end of a group of several genes that are transcribed together |
|
|
Term
| How is promotion different in bacterial and eukaryotic cells? |
|
Definition
-in bacteria, the holoenzyme (sigma facter + RNA polymerase) binds directly to the promoter
-in eukaryotes, accessory proteins fist bind to the promoter and then recruit a specific RNA polymerase (1, 2, or 3) |
|
|
Term
| What does the basal transcription apparatus consist of? |
|
Definition
-RNA polymerase
-general transcription factors
-complex of proteins called the mediator |
|
|
Term
| What is the first step in initiation of transcription in eukaryotes? |
|
Definition
| TFIID (transcription factor) binds to the TATA box because of its TBP (TATA-binding protein) |
|
|
Term
| Who revealed the molecular structure of eukaryotic RNA polymerase II and its function? What year did this person receive the Nobel Prize? |
|
Definition
-Roger Kornberg
-received Nobel in chemistry in 2006 |
|
|
Term
| How does RNA polymerase I know when to terminate? |
|
Definition
| requires a termination factor like rho, however this termination factor binds to a DNA sequence downstream of the termination site |
|
|
Term
| How does RNA polymerase II know when to terminate? |
|
Definition
| -uses Rat1 (a 5'-3' exonuclease) which degrades RNA and RNA polymerase until a termination sequence is reached |
|
|
Term
| How does RNA polymerase III know when to terminate? |
|
Definition
| -transcription is ended after a terminator sequence that produces a string of uracil is transcribed -similar to Rho-independent termination in bacterial cells |
|
|
Term
| Who came up with the "one gene, one enzyme" hypothesis? What year? |
|
Definition
-in the 1940s
-Beadle and Tatum |
|
|
Term
| What is the "one gene, one enzyme" hypothesis? |
|
Definition
| -says that genes function by encoding enzymes, and each gene encodes a separate enzyme |
|
|
Term
| How are amino acids joined? |
|
Definition
|
|
Term
| What are 2 common secondary structures of proteins? |
|
Definition
-alpha helix
-beta pleated sheets |
|
|
Term
| What is the quaternary structure of a protein? |
|
Definition
| -the interaction of 2 or more polypeptide chains |
|
|
Term
| Who developed a method for identifying the amino acid specified by a homopolymer? What year? |
|
Definition
-1961
-Nirenberg and Matthaei |
|
|
Term
| What is the wobble hypothesis and who came up with it? |
|
Definition
-1966
-Francis Crick
-says that base pairing between codon and anticodon can occur in which the third (3') position of the codon allows more than one codon to pair with the same anticodon |
|
|
Term
| What is the reading frame usually set by? |
|
Definition
|
|
Term
| What is the start codon and what do it code for? |
|
Definition
|
|
Term
| What are the 3 stop codons? |
|
Definition
| UAA, UAG, UGA (do not encode for anything) |
|
|
Term
| What are the 3 sites on the ribosome used for translation? |
|
Definition
-A (aminoacyl)
-P (peptidyl)
-E (exit) |
|
|
