Unit 1: DNA Structure Flashcards
What two experiments confirmed that DNA was the genetic material of bacteria, viruses, and eukaryotes ?
1) Griffith experiment
2) Hershey chase experiment
Describe the Griffith Experiment
Griffith used two bacterial strains of streptococcus pneumonia to infect mice.
-one of the strains, the S strain was the virulent one and would kill the infected mice, while the other was the R strain that was harmless.
The reason the S strain was virulent was b/c this particular bacterial could produce a polysaccharide capsule that would protect it from the host immune system. The R strain on the other hand did not have this capsule and hence could not evade the host immune system and thus would be destroyed.
one of the most surprising experiments was when he injected a heat killed S bacteria and a live R bacteria into a healthy mouse. He expected the mouse to live, as the harmful bacteria was already killed prior to injection. Instead he found was that the S type had the same smooth coat as the S strain. This meant that somehow the property of the dead bacteria was transferred over to the R bacteria transforming it such that it could now make the smooth polysaccharide and thus make it very violent DNA.
What is the transforming principle?
genetic properties can be transferred from one bacterial strain to another by extracting DNA from the first strain and adding it to the second strain
The DNA that is taken up by a bacterium
How did phage infection show that DNA is the genetic material of viruses?
When the DNA and protein components of bacteriophages are labeled w/different radioactive isotopes, only the DNA is transmitted to the progeny phages produced by infecting bacteria
Describe the Hershey Chase experiment:
This experiment was trying to distinguish between protein and DNA being the genetic material of viruses. This experiment uses T2 bacteriophages that had either their DNA radioactively labeled with P32 or protein labeled with S35. Following infection, the bacteria were subjected to centrifugation with two fractions separated. One fraction contained the virus capsules that were on the outer surface of the bacteria and the other fraction was the bacteria itself. The first fraction contained all the S radioactive label while the second fraction which went into the bacteria carried the P radioactive label. This demonstrated that the viral DNA entered the bacteria was where replication and incorporation into the progeny phage occur thus confirming the DNA is the genetic material of virus
Through what process do eukaryotic cells take up foreign DNA and incorporate it into its own genome and expression of the DNA results in a new trait
through transfection.
Eukaryotic cells can acquire a new phenotype as the result of transfection by added DNA
A nucleoside consists of a..?
purine or pyrimidine base linked to the 1’ carbon of a pentose sugar
A nucleotide consists of a..?
of a nitrogenous base, pentose sugar, and a phosphate group. The pyrimidine or purine linked to the sugar is called a nucleoside.
What are two differences between DNA and RNA ?
DNA: A-T, C-G
RNA: U-T, C-G
Another difference between DNA and RNA is in the group at the 2’ position of the sugar
-DNA has a deoxyribose sugar (2’H); RNA has a ribose sugar (2’-OH)
Where is the phosphodiester bond between nucleotides formed? How does this affect how the DNA chain is extended?
between the hydroxyl group of the 3’ carbons of the growing chain and the phosphate group on the 5’ carbon of the incoming nucleotide. Thus the chain is always extended in the 5’-3’ direction with the top end of the chain having the free 5’ end and the growing end of the chain having a 3’ end
What is the Watson-Crick DNA form?
B form of DNA which consists of two anti-parallel strands that maintain the same width throughout the entire length of the molecule b/c purine will always pair with pyrimidine and vice versa in the complementary AT and GC base pair
How many hydrogen bonds form between AT and CG pairs?
A-T: 2 hydrogen bonds
C-G: 3 hydrogen bonds
What is meant by complementary base pairing?
base pairs match up in the pairing reactions in double helical nucleic acids
A-T in DNA
A-U in RNA
C-G
explain major and minor groove
The double helix has a major groove and a minor grove. When the helix is twisted, DNA will have areas where the backbones are further apart (major groove) alternating w/areas where the backbones are closer together (minor).
Proteins that regulate transcription or replication bind to which groove, why?
the major groove b/c there would be less steric hindrance from the backbones
The degree of DNA winding can be affected by?
confirmation of the DNA helix and proteins bound to specific sites on the DNA
What is meant when DNA is overwound?
B-form DNA that has fewer than 10.4 base pairs per turn of the helix
What is meant when DNA is underwound?
B-form DNA that has more than 10.4 base pairs per turn of the helix
When does supercoiling occur in DNA?
when DNA bends over on itself (crosses over its own axis) causing more tension, twisted and condensed form, and hence more energy than the stable relaxed form of DNA
-supercoiling occurs only in ‘closed’ DNA w/no free ends.
Why is supercoiling needed?
1) to compact the large amount of DNA found w/in a cell
2) in prokaryotes supercoiling plays a role in replication initiation
True or False: closed DNA is either circular DNA or linear DNA in which the ends are anchored so that they are not free to rotate
TRUE
The linking number (L) is the sum of what?
The sum of twist (T) and writhe (W)
L= T + W
where twist (T) represents the number of helical turns the two strands make and writhe (W) represents the supercoiling of the helix
In a relaxed circular molecule where there is no supercoiling, the linking number would be equal to what?
it would be equal to the twist (T) since W would equal 0.
TRUE OR FALSE: A linking number can have different combinations of T and W provided their sum is unchanged
True, the linking number remains constant as long as the closed DNA is intact and there have been no breaking and reforming of bonds
If a linking number decreases this reflects?
a combination of negative supercoiling or underwinding
If a linking number increases this suggests what?
positive supercoiling or overwinding
The linking number typically remains constant, but can change, what can lead to these changes?
the linking number can be changed only by breaking and reforming bonds in the DNA backbone.
Why is DNA replication called semiconservative?
b/c in the daughter strands that are produced, 1 strand is always the parental strands (which serves as the template for synthesis of the daughter strand)
-DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand . The sequence of the daughter strands are determined by complementary base pairing w/the separated parental strand
What did they Meselson-Stahl experiment demonstrate?
used “heavy” isotope labeling to show that the single polynucleotide strands is the unit of DNA that is conserved during replication
How is DNA converted into RNA?
by transcription
How is RNA converted into DNA?
reverse transcription
What is an RNA polymerase?
an enzyme that synthesizes RNA using a DNA template (formally described as DNA-dependent RNA polymerase)
How is genetic information provided?
either by DNA or RNA (virus have RNA as genetic material and covert the RNA to DNA by reverse transcription using an enzyme called reverse transcriptase)
What is meant by the central dogma?
information cannot be transferred from protein to protein or protein to nucleic acid, but can be transferred between nucleic acids and from nucleic acids to protein.
—>transfer of information into a polypeptide is irreversible
The translation of a RNA into a protein is said to be?
unidirectional; information is transferred from DNA to RNA to Protein
TRUE OR FALSE: Denatured single strands of DNA cannot renature
FALSE; denatured single strands of DNA can renature to give the duplex form
What happens when DNA molecules are heated?
it will cause the strand to separate or what is referred to as denaturation.
What is the melting temperature (Tm)?
every molecule has a specific melting temperature which is the midpoint of the temperature range for denaturation.
What happens when temperature is lowered below the Tm?
the two strands come together (aka anneal) and are renatured to form the original duplex
How can denature DNA renature to form a duplex?
Due to complementary base pairing between the two strands, which can renature or anneal (inter or intramolecularly)I A-T are linked by two hydrogen bonds, while CG are linked by three hydrogen bonds. Hence the DNA molecule has a higher CG content and will also have a higher Tm as more energy is needed to separate triple hydrogen bonds then double hydrogen bonds. This hybridization of base pairing can be between one DNA strand and another DNA strand or between DNA and RNA or RNA and RNA
TRUE OR FALSE: the greater the extent of complementary the greater the degree of hybridizaiton
TRUE; the ability of two single-stranded nucleic acids to hybridize is a measure of their complementarity
Different forms of DNA do not affect which key/basic properties of DNA?
- strand complementarity
- antiparallel strands
- AT two hydrogen bonds versus GC pairs three hydrogen bonds
How can a DNA molecule adopt different structures? What causes structural variatons?
structural variation in DNA reflects three things: the different possible conformations of the deoxyribose (sugar pucker), rotation about the contiguous bonds that make up the phosphodeoxyribose, and free rotation about the C-1’-N-glycosyl bond
What different configurations can the sugar pucker of DNA hold?
either the endo or exo form.
in both structures 4 of the 5 carbons that form the ring lie in one plane. The 5th carbon of that ring either the C2’ or C3’ can be on the same side of the plane as the C5’ (endo) or on the opposite side (exo)
How can the backbone of DNA have different configurations?
The confirmation of the nucleotide can be affected by the rotation about 7 different bonds. 6 of these bonds rotate freely. The limited rotation about bond 4 gives rise to ring pucker (endo and exo), in which one of the atoms in the five-membered furanose ring is out of the plane descried
How does the rotation about the C1N glycosyl bond change DNA conformaton?
bond 7, which is the glycosyl bond can either be in anti or syn form. For purine bases in nucleotides, only two conformations w/respect to the attached ribose units are sterically permitted, (Anit and syn). Pyrimidines generally occur in the anti conformation
Why are pyrimidines generally restricted to the anti conformation?
b/c of steric interference between the sugar and the carbonyl oxygen at the C2 of the pyrimidine
Why is the Watson-Crick structure the standard reference for DNA?
b/ it is the most stable under physiological conditions compared to A and Z DNA.
Under what conditions is A DNA observed?
seen under dehydrated conditions.
How is A DNA similar to B DNA?
Similar to B DNA in that it is a right handed helix.
A DNA Helix: Wider w/ 11 bases per unit
B DNA helix: 10.5 bases
There are difference in the sugar bucker for these as well as the tilt of each base to the helical axis is quite steep for A DNA being 20 degrees. These changes make the major group deeper and the minor group shallower compared to B DNA.
How is Z DNA different than A and B DNA?
the main difference being the twist is now left handed the structure is most slender and elongated and has more of a zigzag appearance the major group is barely seen while the minor group is narrow and deep it is not very clear if a DNA is seen in cells however there is evidence of the Z form in certain short stretches of DNA and has been seen in both prokaryotes and eukaryotes
What is a palindromic sequence w/in DNA?
it is a self complementary strand and it reads the same forward in one strand and the reverse on the complimentary strand.
palindromic b/c of its self-complementary can form hairpin and cruciform structures
What is a mirror repeat?
an inverted repeat occurs on the same strand
a mirror repeat cannot form hairpin or cruciform structures b/c they do not have complementary sequences w/in the strand
What is triplex DNA? What is another name for this?
when the Watson-Crick base pairs form additional hydrogen bonds w/functional groups that are available in the major groove of the helix.
For example T-A-T or C-G-C, this type of pairing is called Hoogsteen pairing.
When do hoogsteen/triplex structures arise?
we see this type of structure confirmation at low pH as well as if there are long sequences of only pyrimidines or purines.
What is the tetraplex structure and when do they occur?
These structures are four strands of DNA coming together and they are seen when there is a high proportion of guanosine residues b/c of the foot bonds formed between the guanine tetraplex
RNA is single stranded but can form different secondary structures, what secondary structures does it form?
Z form has been observed. The most common secondary structures are the hairpin and loop structures. a lot of non-watson crick pairing, as in guanine hydrogen bonded uracil and they hydroxyl groups of ribose forming hydrogen bonds with other groups
What information did Watson and Crick used to come up with the model of structure of DNA molecule?
Watson and Crick used data from the X Ray diffraction studies carried by Rosalind Franklin and Maurice Wilkins which told them that the molecule was a Helix this along with the results of Chargaff’s experiments which showed that the A’s must equal T’s and G’s equals C’s allowed Watson and Crick to postulate a 3-dimensional model of the DNA molecule that would satisfy all of the available data
