A double chain of NUCLEOTIDES
-each nucleotide is composed of a 5 carbon RIBOSUGAR, a phosphate, and a base (ADENINE, THYMINE, GUANINE, OR CYTOSINE)
-the ribosugar and phosphate group make up the "backbone" of the DNA strand
-the ribosugars are bound together by the phosphate groups, which connects to the 5th carbon of one sugar, and to the 3rd carbon of another sugar (this is known as 5' to 3'); this creates the DNA strand
-the two DNA strands run in opposite directions (ANTIPARALLEL)
The two BASE PAIRS are located the middle, with the "backbone" strands making up the outside of the structure
-these nucleotide base pairs are held together by hydrogen bonds
Adenine (A) always pairs with Thymine (T), Guanine (G) always pairs with Cytosine (C)
Due to the two antiparallel strands, as well as the bonded base pairs, the DNA has a DOUBLE HELIX shape
Textbook: Figure 7.1
Begins at a specific location (the ORIGIN), and moves outwards in both directions
-various enzymes, called HELICASES, break the hydrogen bonds between the bases of the two DNA strands, creating REPLICATION FORKS
-then, DNA POLYMERASE, an enzyme, moves along the replication fork, synthesizing new DNA strands that are complementary to the original ones (ex. A for T,G for C); they also "proofread" the strand, and correct errors
DNA polymerase can only add nucleotides to the 3' end of a DNA strand -therefore, only one strand of the original DNA can be a template for DNA replication; the LEADING STRAND, which runs in a 5' to 3' direction
For the LAGGING STRAND, which runs in a 3' to 5' direction, DNA synthesis must be DISCONTINUOUS
-RNA primer is attached to the parent DNA
-DNA polymerase then synthesizes a fragment of DNA starting at the RNA primer; this small segment is known as an OKAZAKI FRAGMENT
-this process is repeated until the entire strand has been replicated
-DNA polymerase will then digest the RNA primer and replace it with DNA
-The fragments are then joined by an enzyme called LIGASE
Ultimately, two separate chromosomes are formed
-each double helix contains one new strand, as well as an old strand of DNA; this replication is called SEMICONSERVATIVE REPLICATION, because one strand of the old DNA goes to each new DNA structure
Textbook: Figure 7.4
In order for a bacterial cell to live, it must produce proteins
-short sections of DNA strands are broken at the base pairs, leaving exposed DNA bases; these serve as templates for transcription
-the enzyme RNA POLYMERASE then binds to one strand of exposed DNA; it knows where to bind due to a sequence of bases in the DNA, which indicates that it is the start of a gene; this is known as a PROMOTER SEQUENCE
-RNA is then transcribed, formed in the 5' to 3' direction
In prokaryotes, transcription takes place in the cytoplasm; in eukaryotes, transcription takes place in the cell nucleus
Eukaryotic cells also process its mRNA before it leaves the nucleus and begins translating; INTRONS, which don't code for proteins, are cut away from the EXONS, which is the region of genes that codes for proteins; the exons are then spliced together
-this does not occur in prokaryotes
Side Note: when mRNA is transcribed from DNA, Uracil (U) binds with Adenine, not Thymine
Textbook: Figure 7.5, 7.6, 7.10
The lac operon consists of regulatory sites, called a PROMOTER, and an OPERATOR, as well as the structural genes used to create enzymes that digest lactose
In the lack of lactose, the operon is turned "off"
-a regulator gene codes for an active repressor protein; this protein binds to the OPERATOR SITE; which sits in between the promoter site (which initiates the transcription of genes), and the genes that will create the enzymes needed to digest lactose
-when RNA polymerase binds to the promoter site to start transcription mRNA, it becomes blocked by the repressor protein, thus blocking transcription
In the presence of lactose, the operon is turned on
-the regulator gene is still coding for active repressor proteins, therefore the repressor proteins still exist
-however, the lactose combines with the repressor proteins, meaning it can no longer bind with the operator site
-RNA polymerase, which has bound to the promoter site, is now free to transcribe the genes necessary to produce enzymes for lactose digestion
-once the enzymes digest the lactose, the repressor proteins are freed up and are able to bind with the operator site, which in turn blocks the transcription of the structural genes necessary to create enzymes for lactose digestion
The repressor protein is a CONSTITUTIVE PROTEIN, because it is always expressed, while every other protein is INDUCIBLE, as they are created under the right conditions
Textbook: Figure 7.14
Back in the 1950s, a lot of scientists were trying to understand mutations; whether antibiotics created mutations, or whether cells spontaneously mutated on their own
This was finally put to the test when scientists created a pure culture that had never experienced antibiotics, then introduced the antibiotic STREPTOMYCIN into the culture
-the scientists then inoculated a plate with cells, and also placed streptomycin into the agar, creating an environment in which only antibiotic resistant cells could live
-every plate had approximately the same number of colonies
At the same time, the scientists inoculated 100 small tubes of liquid medium with the same pure culture bacteria, and allowed each colony to grow to it's maximum growth
-samples were then taken out of every tube and were used to inoculate plates that contained streptomycin
-the scientists found that there was a much greater fluctuation in the number of colonies per plate; some plates had many colonies, some had few, and some had none at all
The scientists were, therefore, able to conclude that mutations were spontaneous and random processes that happened at different times, as could be seen by the fluctuation of resistant strains per each flask
-ex. plates with many colonies probably came from samples that had mutations early on, therefore, the mutated population had time to grow
Textbook: Figure 7.23
Initially, flu-like symptoms are presented, but the infected individual can usually recover
-if antiviral therapy is initiated at this stage, a healthy immune system can be maintained
Over time, the immune system begins to weaken as the virus constantly buds away from the t-cells, thus making it weaker and weaker
-this is when people can develop lots of problems with infections such as shingles, herpes infections, skin problems, or even Kaposi's sarcoma
-there are also OPPORTUNISTIC infections as well; the human body's normal flora begins to create problems, as they are now unregulated; this leads to things like fungal infections
Ultimately, the metabolism in people becomes compromised and people begin to waste away, until they cannot support their health anymore and succumb
A virus that is composed of 8 fragments of RNA
-these code for viral proteins
The proteins HEMAGGLUTININ and NEURAMINIDASE are required for the virus to be infectious
Influenza is constantly changing, as genes coding for proteins might mutate, thus creating different strains; these changes are known as ANTIGENIC DRIFT
If two different viruses infect a host cell simultaneously, there is a chance for the two strains to combine and create new strains; this is called ANTIGENIC SHIFT
-this is incredibly dangerous, as for example, if "bird flu", which is rare to infect humans but very lethal, were to combine with influenza strains that can infect humans, it would create a catastrophe
Vaccines are created every year with different strains that are most common for that year
-created in embryonated chicken eggs, but this is an extremely slow and inefficient process and leads to vaccine shortages
-currently, a tissue culture system is being developed to create more efficient viruses
Textbook: Pages 672-678
1. Microorganisms can control their metabolism by feedback inhibition, enzyme induction and enzyme repression.
2. An example of enzyme induction is the lac operon being turned on when lactose is present. Enzyme induction involves a repressor protein transcribed from the regulator gene as well as the lac operon. This operon contains a promoter, operator and 3 structural genes for lactose metabolism.
3. If glucose and lactose are both present in a cell simultaneously, the cell will metabolize glucose first due to catabolite repression.
4. The operon for tryptophan synthesis is an example of enzyme repression. In this case, if levels of tryptophan are high, it can bind to the repressor for the tryptophan operon, which activates the repressor, so it can now bind to the operator region thus preventing transcription of that operon. When the level of tryptophan is low, the repressor is not bound to tryptophan and therefore is inactive so the operon can be turned on.
5. Chemicals like alklylating agents, deaminating agents and base analogs cause point mutations whereas acridine will cause frameshift mutations.
6. The fluctuation test proved that antibiotic resistance occurs spontaneously and at random. In other words, mutations are not induced by exposure to a particular substance, like a antibiotic, but occur spontaneously.
7. The polymerase chain reaction (PCR) allows one to make multiply copies of a particular nucleotide sequence in a DNA sample. Unique DNA primers are used that can base pair at the end of each DNA strand which contains the specific DNA sequence that one wants to amplify. The DNA strands are separated from exposure to a high temperature so one needs to add DNA polymerase that will work at high temperatures and synthesize each strand of the DNA adding nucleotides from the primer. This process is repeated a number of times resulting in an amplified DNA fragment that can be detected by adding certain reagents to the reaction. In the future, this procedure will become very important in the identification of a particular microorganism in a clinical sample. One can make unique DNA primers for that specific microorganism which one suspects might be in the sample. If a DNA amplified product is produced, then one would know that the microorganism is present. There are 2 advantages of using this method rather than performing diagnostic tests (as described in chapter 6) to determine what organism is in the clinical sample. 1.You do not need to have a pure culture of the organism to perform PCR. 2. The PCR method is much quicker than performing diagnostic tests.
8. When gene transfer occurs the chromosomal DNA from a donor cell is taken up by a recipient cell. A recombination event occurs on the recipient chromosome which allows for the incoming DNA to get incorporated into the recipient chromosome.
9. The 3 types of lateral transfer that occur in bacteria are called transformation, transduction and conjugation. Transformation involves "naked" DNA, transduction involves bacteriophages and conjugation involves cell to cell contact.
10. The first example of transformation was seen in the experiment in which Griffith used Streptococcus pneumoniae. He took the wild type capsulated virulent form of the bacteria that was heat killed and mixed it with the live nonvirulent (no capsule) strain and recovered the capsulated form of the organism after he put the mix into the host mouse. At the time, it was not know that DNA carried the genetic information but Griffith did demonstrate that the nonvirulent strain was transformed with information to make a capsule from the heat killed strain.
11. During transformation bacteria can take up donor DNA when it makes the competence factor that facilitates entry of the naked DNA into the cell. The naked DNA must recombine with the recipient DNA at homologous sequences on both types of DNA so that the naked (donor) DNA can be expressed in the recipient cell.
12. Transformation occurs in a wide variety of organisms. In nature, it gives the the organism a chance to pick up new traits which could help it survive in a number of conditions that it might encounter in the environment. It is possible that some of the drug resistance that is seen in bacteria is due to a transformation event.
13. Transduction involves bacteriophages which are viruses that infect bacteria. Bacteriophages have a specific host range so bacteriophage that can infect Salmonella, for example, will not infect E.coli.
14. Phage DNA that is incorporated into host bacterial DNA is called a prophage. The host bacterium carrying the prophage is said to be lysogenic.
15. .The basic components of a virus are a nucleic acid (DNA or RNA), capsid , envelope and possibly spikes projecting from the virion particle.
16. A virus is classified into a Family, Genus and Species. The ICTV requires the common English name be used to designate a viral species.
17. Viruses can be cultured in animals, embryonated eggs (Influenza Virus propagated this way), and Tissue Culture. The damage caused to tissue culture cells by the virus is called the Cytopathic Effect (CPE).
18. Prions (PrP) are small proteinaceous infectious particles. There is a normal form of this protein in human cells (especially brain) and if it comes in contact with the misfolded prion proteins (PrP), it is thought that the wild type protein is converted to the misfolded form. The misfolded proteins start to stick together in fibrils. Ultimately this leads to brain cell death and to the diseases collectively referred to as transmissible spongiform encephalopathies. These diseases are fatal and on autopsy, one can see holes in the brain tissue. Kuru, CJD, new-variant CJD, Scrapie and Elk Wasting Disease are some of the diseases caused by prions.
1. There are a number of terms in chapter 7 that pertain to DNA replication that you should be able to explain, such as replication fork, leading DNA strand, lagging DNA strand, Okazaki fragments, 5-prime to 3-prime direction, semi-conservative replication and antiparallel strands.
2. How does reverse transcription differ from transcription?
3. The following are a number of terms associated with mRNA that you need to know: codon, nonsense codon, genetic code and start codon.
4. What 2 chemical features make a single strand of DNA different from a single strand of RNA?
5. Describe what roles the 3 types of RNA play in translation. What RNA would contain the anticodon? What is a polyribosome?
6. Eukaryotic mRNA are usually made containing both exons and introns. The introns are spliced out and the exons joined to make the mRNA which will be translated. What benefit does having mRNA that needs to be spliced give to the eukaryotic cell?
7. What is an operon?
8. Explain how the lac operon and repressor work together under conditions when lactose is present and when it is not present
9. Do all genotype changes result in a phenotype change?
10. Why are frameshift mutations usually more deleterious to a cell than a point mutation?
11. Which organism is considered wild type, the auxotroph or prototroph?
12. UV light causes pyrimidine dimer formation in DNA. What can microorganisms do to remove them?
13. The Ames Test is used to screen for potential mutagenic properties of substances/chemicals. How does it work?
14. Gene transfer refers to the movement of genetic information between organisms. Know the difference between lateral gene transfer and vertical gene transfer.
15. Bacteriophages are considered either virulent or temperate. Know the difference between both.
16. Know the difference between generalized transduction and specialized transduction and how virulent and temperate bacteriophages are involved in transduction.
17. Conjugation requires cell to cell contact to transfer a F+ (Fertility plasmid) to a F- cell. How does a successful conjugation event convert a F- strain to a F+ strain?
18. How do Hfr and F' cells transfer their DNA to a F- strain?
19. Plasmids are circular, extra chromosomal, double stranded DNA molecules. Plasmids can provide new traits to an organism through the genes they carry in their DNA. What are some of the new traits that an organism may acquire from a plasmid?
20. Why can transposable elements cause mutations? How do they contribute to the spread of antibiotic resistance?
21. Through recombinant DNA technology, scientists have been able to get microorganisms to express useful human proteins that are presently used in health care. What are the 4 basic steps needed to bring a human fragment of DNA into a plasmid, which will be introduced into a recipient bacterium for ultimate expression of that human protein. Understand the importance of both the plasmid and restriction enzymes in this technique.
22. Know the 5 steps of viral replication for both animal viruses and bacteriophages.
23. What would a growth curve for a bacteriophage look like?
24. What are the two ways a enveloped virus can enter a human host cell?
25. How does replication of a DNA virus differ from a RNA virus?
26. Why does a (-) sense RNA virus need to bring an enzyme called transcriptase into a host cell but the (+) RNA virus does not need to?
27. Define Viral Latency.
28. Define Teratogenesis. What viruses are known to cross the placenta?
29. Many viruses are associated with human cancers. Integration of viral DNA into host DNA can cause expression of viral proteins (oncogenes) which results in unregulated growth of the host cells. RNA tumor viruses may even carry genetic information from a host cell that it previously infected. This genetic information (proto-oncogene) may become expressed in the new host cell and lead to uncontrolled growth. Know which viruses are associated with cancer such as Papillomavirus.