Chapters 13,14,15 test Flashcards
What was The major achievement of James Watson and Francis Crick?
They made an elegant double-helical model for the 3 dimensional structure of DNA
What make nucleic acids unique in nature?
Their ability to direct their own replication from monomers
What was the key factor in determining the identity of genetic material? why?
Choosing the appropriate organisms to study, like bacteria and viruses because they are simpler
What is transformation? Who first used this term in genetics?
discovered by Frederick Griffith, transformation is a change in genotype and phenotype due to assimilation of external DNA by a cell
What are bacteriophages?
Called phages for short, these are viruses that infect bacteria that are used to study DNA
What is a virus?
An organisms that is basically just DNA(or sometimes RNA) enclosed within a protective coat that must infect other cells and take over their metabolic machinery to reproduce
Who discovered whether viruses used DNA or protein to infect and reprogram other cells and how?
Alfred Hershey and Martha Chase. They did this by tagging phage protein with a radioactive isotope of sulfur and tagging phage DNA with radioactive phosphorus. They found that phage DNA entered the the host cells and protein did not
Why was Hershey and chase’s experiment important and what were their conclusions?
They concluded that DNA injected by the phage must be the molecule carrying genetic information that makes the cells produce new viral DNA and proteins. Their study was important bc it provided powerful evidence that nucleic acids rather than proteins are hereditary material, at least viruses.
How was Erwin Chargaff significant?
He provided further evidence that DNA is the genetic material. He first discovered that the base ratios that compose DNA vary in different species, a diversity that was believed to be absent made DNA a more credible candidate to be genetic material. He also noticed that the number of adenines was close to the number of thymines and the number of guanines almost equaled the number of cytosines. These discoveries resulted in Chargaff’s rules(which are these 2 findings)
What dies antiparallel mean? what part of DNA is this applicable to?
Antiparallel means that they run in opposite directions parallel to each other. This sugar phosphates run in the DNA double helix structure
Why is adenine always paired with thymine and guanine with cytosine?
A and G are purines, nitrogenous bases with 2 rings. C and T are pyrimidines, nitrogenous bases with 1 ring. Purines are about twice as wide as pyrimidines, so purine-purine pairs are too wide and pyrimidine-pyrimidine pairs are 2 narrow to account for the uniform 2nm diameter of a double helix. Furthermore, each base has chemical side-groups that can form H bonds with it’s partner only
What is the model of DNA that Watson and Crick came up with for their hypothesis on DNA replication?
The semiconservative model
What are the origins of replication?
The particular sites where DNA replication begins, these are short patches of DNA having a specific sequence of nucleotides. Proteins that initiate DNA replication attach to the DNA and separate the two strands and opening up a replication bubble
What is a replication fork?
A Y-shaped region where the parental strands of DNA are being unwound
What are helicases?
Enzymes that untwist he double helix at the replication forks, separating the two parental strands and making them available as template strands
What are single-strand binding proteins?
Proteins that bind to the unpaired parental strands after they separate, keeping them from repairing
What is topoisomerase?
A enzyme that helps relieve the strain caused by the untwisting if the double helix that causes tighter twisting and strain ahead of the replication fork
How is DNA replication similar and different bacteria and prokaryotes?
Bacteria have one origin of replication, while eukaryotes have multiple to speed of the process. Both of these processes are similar in that replication proceeds in both directions from each origin
What is a primer?
The short stretch of RNA that is the initial nucleotide chain produced during DNA synthesis.
What is primase? What does it result in?
The enzyme that synthesizes a primer by starting a complementary RNA chain from a single RNA nucleotide, adding RNA nucleotides one at a time, using the parental DNA strand as a template. The completed primer is based paired to the template strand and the new DNA strand will start from the 3’ end of the RNA primer
What are DNA polymerases?
Enzymes that catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain. Most require a primer and a DNA template strand along which complementary DNA nucleotides lines up
What are 2 examples of DNA Polymerase?
DNA Polymerase III and DNA Polymerase I, they play a major role in DNA replication in E. coli.
III: adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides complementary to the parental DNA strand to the growing end of the new DNA strand
What consists of each nucleotide added to a growing DNA strand?
A sugar attached to a base and 3 phosphate groups
What is dATP and how is it different from ATP?
dATP is the adenine nucleotide used to make DNA. It is different from ATP because its sugar is deoxyribose instead of ribose
What makes the nucleotides used for DNA synthesis chemically reactive?
their triphosphate tails have an unstable cluster of negative charge
What exergonic reaction helps drive the polymerization reaction?
As each monomer joins the growing end of a DNA strand, two phosphate groups are lost as a molecule of pyrophosphate then they undergo hydrolysis to become two inorganic molecules of phosphate
What does a helix being antiparallel affect replication?
Due to the structure, DNA can only add to the free 3’ end of a primer or growing DNA strand, never to the 5’ end. Thus, the new DNA strand can only elongate in the 5’ to 3’ direction
What is the leading strand?
The DNA strand made by the continuous addition of nucleotides to the new complementary strand as the replication fork progresses
How many primers are needed for DNA pol III to synthesize the leading strand?
One
What is the lagging strand?
The template strand elongating away from the replication fork
What are okazaki fragments?
The fragments in which the lagging strand is synthesized discontinuously by.
What is different about primers on the leading and lagging strand?
One primer is required on the leading strand, whereas each okazaki fragment must be primed separately on the lagging strand
What is the role of DNA pol III and I on lagging strands?
DNA pol III forms the okazaki fragment after the RNA primer. DNA pol I replaces the RNA nucleotides of the adjacent primer with DNA nucleotides
What is DNA ligase?
An enzyme that joins the final nucleotide of the replacement DNA from DNA pol I to the first DNA nucleotide of the Okazaki fragment, joining sugar-phosphate backbones of all okazaki fragments into a continuous DNA strand
Why is the railroad track representation if DNA inaccurate?
- The various proteins in DNA replication actually fork a single large complex
- The DNA replication complex may not move along the DNA, it may actually be vice versa
Why is DNA replication so accurate?
During replication, DNA polymerases proofread each nucleotide against its template as soon as it is added to the growing strand. If an error is found, the nucleotide is removed and synthesis is resumed
What is mismatch repair?
When enzymes other than DNA polymerase remove and replace incorrectly paired nucleotides that DNA polymerase missed
What is nuclease?
A DNA cutting enzyme that cuts out a damaged segment of DNA and the resulting gap is filled with nucleotides, using DNA polymerase and DNA ligase
What is nucleotide excision repair?
A DNA repair system involving nuclease and its function
What makes a mismatched nucleotide replication permanent?
replication
How has mutation effected evolution?
A low mutation rate allows evolution and diversity of species we see today. Some mutations are beneficial and are ultimately responsible for the appearance of new species
What is telomerase?
An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells, restoring them to their original length and compensating for the shortening that occurs in replication
How are bacterial and eukaryotic chromosomes different?
Eukaryotic chromosomes consist of one linear DNA molecule associated with a large amount of protein. Bacteria consist mostly of one double stranded circular DNA molecule
How is a nucleoid and a nucleus different?
The nucleoid is not surrounded by membrane and the nucleus is
What is heterochromatin?
Interphase chromatin that is visible as irregular clumps with a light microscope. This is less accessible to the machinery responsible for transcription
What is euchromatin?
Less compacted and more disperse chromatin
What are the 4 most common types of histones in eukaryotes and what do they do?
H2A, H2B, H3 and H4. They are critical for DNA packing
What is a nucleosome?
(10nm) Unfolded chromosome resembling “beads”, the basic unit of DNA packing. These consist of DNA wrapped twice around a protein core composed of two molecule of each histone type and a histone tail extending from the nucleosome
What is a 30-nm fiber?
The next level of packing from nucleosomes/10-nm fibers. A fifth histone, H1, becomes involved at this level. The histone tails of one nucleosome and the DNA linker of another interact, coil, and fold to form a 30nm fiber, this is prevalent in the interphase nucleus
What are looped domains?
(300-nm fiber) The next level from 30 nm fibers. The 30nm fibers form loops called looped domains attached to a chromosome scaffold composed of proteins, making up the 300nm fiber
What is the metaphase chromosome?
The next level of packing from a 300 nm chromosome. The looped domains coil and foil to form a 700nm chromatid. Particular genes always end up located at the same places
What is nucleic acid hybridization?
The base pairing of one strand of nucleic acid to a complementary sequence on another strand
What are plasmids?
small circular DNA molecules that replicate separately from the bacterial chromosome
What is recombinant DNA?
A DNA molecule formed when segments of DNA from 2 different sources-often different species-are combined in a test tube
What is gene cloning?
The production of multiple copies of a single gene
What is the most common way to clone DNA in a laboratory?
Using E. coli plasmids to make a recombinant bacterium
What are restriction enzymes?
Enzymes that cut DNA molecules at a limited number of specific locations. They protect bacteria by cutting up foreign DNA from other organisms or phages
What is a restriction site?
A specific, short DNA sequence that a restriction enzyme recognize where it cuts the DNA