EXAM 2 QUESTIONS Flashcards
Name at least 4 structural predictions made by Watson/Crick DNA model.
Base pairs were complementary
The structure formed a Double Helix
The helix was Right-handed
A pairs with T; G pairs with C
The diameter of DNA is 20 Angstroms.
Base pairs are perpendicular to the strands and lie flat.
The strands are antiparallel, where one runs from 3’-5’ and the other 5’-3’.
What are the 3 classes of “functional” (non-mRNA) RNAs?
Briefly describe the role of each class of functional RNA.
tRNA: brings the correct amino acid to the mRNA during translation
rRNA: major component of ribosomes
snRNA: helps process RNA transcripts (especially, helps remove introns).
Discuss the experimental evidence for the semi-conservative replication of DNA determined by in vitro experiments in the bacteria E.Coli.
The scientist started with heavy N-15 DNA, and allowed it to mix with the light N-14 DNA.
The first round of replication yielded identical DNA strands that had one full parent N-15 strand and one new N-14 strand.
These results ruled out the possibility of conservative replication because they were hybrids.
One more trial was needed to rule out the dispersive model of replication.
The second round yielded light-heavy DNA hybrids and light DNA (14/15-N and 14-N).
These results ruled out the dispersive model because the dispersive model would have only yielded hybrids.
Briefly state and describe the 4 primary ingredients that, along with DNA polymerase I, are needed for the in vitro system.
Buffering, temperature, and nonspecific ion concentrations are conditions, not ingredients.
!!!!???
Taken, in part, from Module 2.2 lecture.
- DNA primers/template with partial complement:
strand of nucleic acid that serves as a starting point for DNA synthesis
-dNTPs:
The building blocks for new strands are deoxyribose nucleoside triphosphates (A,T,C, or G)
-MgCl2: (or Mg++)
part of the active site. It helps bind the nucleotides which the DNA polymerase uses to copy the template strand and join to make new DNA
-Phosphate source:
The phosphate bonds to the nucleotide triphosphates and provides the energy
Kornberg used the phage PhiX174 to demonstrate DNA pol 1 was able to produce biologically active DNA in vitro.
Describe in sufficient detail the experimental methods that he used to draw the conclusions in DNA pol 1 could produce biologically active DNA.
The last part comes directly from slides.
The phage would insert the (+) form of its genetic information inside the host. The host would make (-) copies. (+) form phages would leave the cell to do it again. Pol I, and no other polymerase was present, but translation occurred accurately.
Single stranded circular DNA (+) strand infects E. coli.
The (+) strand directs replication of the (-) strand in E. coli, resulting in double-stranded duplex or replicative form (RF).
(+) strands are produced and packaged into viral coats to form mature virus particles.
Final (+) strand of øX174 infected E. coli and produced infectious mature phage particles.
DNA replication was accurate; any alteration the bases of øX174 would have probably rendered it non-viable.
What are 3 ways that miRNA can influence gene expression?
miRNA….
- Represses translation,
- Triggers mRNA degradation,
- Represses transcription of specific genes and larger regions of the genome using
RITS. - Works with RITS for chromatin remodeling and transcriptional silencing.
- miRNA has a role in splicing, and it can get mRNA destroyed. It works with snRNA to regulate mRNA.
correct answer, got from TA:
- degrades mRNA
- condenses chromatin
- prevents processing of ribosome
What experimental methods led Avery, McCarthy, & Macleod to determine that DNA was the “transforming material” in their classic experiments?
They introduced enzymes to the mixtures to degrade one component at a time and see if the genetic material was still passed on or not.
If the genetic material passed to the next generation, then the substance that the enzyme degraded was not the transforming material.
RNAse, for example, was introduced to remove all RNA; the genetic material still passed on, so RNA could not be the genetic material.
DNAse removed all DNA, and no genetic information passed on, so the scientists knew that DNA held the genetic information.
They performed an experiment where they took a large sample of IIIS, centrifuged, and heat killed it.
After that they excised and removed the proteins, carbohydrates, and lipids.
When joined to the active substrate IIR, transformation occurred.
They then treated with protease to get rid of all the remaining protein.
Transformation still occurred proving that protein was not the transforming material.
They then treated with ribonuclease.
Transformation still occurred proving that RNA was not the transforming material.
Lastly. they treated with deoxyribonuclease (DNAse) to get rid of the DNA and no transformation occurred.
This proved that DNA was the transforming molecule.
An organism has a A + T content of 50%.
What is the percentage for C?
25%
Which of the following DNA double helices would be more difficult to separate into single-stranded molecules by treatment with heat (which breaks hydrogen bonds)?
Indicate the reason for your choice.
A:
GCATTAGGGCATCCC
CGTAATCCCGTAGGG
B:
TTAGCGTTATAGCAT
AATCGCAATATCGTA
DNA molecule A would be most difficult to separate, because it has a higher G-C content.
Molecules B has a higher A-T content.
DNA molecule A has a higher A-T content. However, G-C pairs are held together by three hydrogen bonds while A-T bonds are held together by 2 hydrogen bonds. Hence, a higher number of G-C pairs gives a double-stranded DNA a higher heat resistance.
Match with best letter choice:
DNA Ligase
i, phosphodiester bonds at DNA nicks
The 5’ cap on an mRNA is important fro all the purposes listed below, EXCEPT for the ___ of an mRNA molecule.
Transcription
Intron Removal
Stability
Initiation of Translation
Transcription
While actually a form of RNA polymerase, this enzyme lays down the initial nucleotides to set up a condition where DNA polymerase can the take over for replication.
Primase
This new strand of DNA has its 3’ end orientated in the Opposite direction as that in which the replication fork travels.
The lagging strand
Assume the following pathway:
Precursor —> K —> C —> B —> Product
Mutations for 3 genes (genes I, II, and III) have been isolated that interrupt this pathway.
Addition of:
B rescues mutations in gene III
K, C, and B rescues mutations in gene II
C and B rescue mutations in gene I
In what order do genes I, II, and III function in this pathway?
II, I, III
Matching terms:
Primase
synthesis of RNA primer
Matching terms:
SSBP
stabilizing single-stranded DNA
Matching terms:
Helicase
Unwinding DNA
Matching terms:
Gyrase/Topoisomerase
Relieve tension in DNA due to supercoiling
Matching terms:
DNA Polymerase III
initiate DNA synthesis
Matching terms:
DNA ligase
connecting Okazaki frgments
Matching terms:
DNA Polymerase I
Filling the gap left after primers are removed
The ribosome is the primary site of
protein synthesis
The anticodon on the tRNA molecule…
binds to the mRNA in a complementary fashion
What is a gene?
A sequence of DNA that encodes a PROTEIN.
How many nucleotides would be expected for a gene coding for a protein with 300 amino acids?
900
Before DNA was known to be the genetic material, scientists knew that genetic material must do or be all of the following, EXCEPT that
genetic material must encode the phenotype.
genetic material must replicate faithfully.
genetic material must contain complex coding information
genetic material must be composed of many different units to account for the variability seen in nature.
genetic material must be composed of many different units to account for the variability seen in nature.
(this was not known before DNA was identified as the genetic material)
Which of the following statements is NOT true concerning RNA and DNA?
a) RNA is more stable than DNA
b) DNA is transcribed into RNA which is translated into protein
c) DNA is permanent in a cell, RNA is temporary
d) The sugar portion of RNA and DNA are different
RNA is more stable than DNA
In the DNA double helix, …
A purine always pairs with a pyrimidine
What enzyme is exploited to produce synthetic mRNAs?
Polynucleotide phosphorylase
Cytosine makes up 28% of the nucleotides in a sample of DNA from an organism.
Approximately what percentage of the nucleotides in this sample will be Thymine?
12
When considering the initiation of transcription, one often finds consensus sequences located in the region of the DNA where RNA polymerase(s) bind.
What are some common consensus sequences?
CAAT, TATA
Translation is directly dependent on all of the following associations EXCEPT _______.
a. complementary base pairing between mRNA and rRNA
b. complementary base pairing between mRNA and tRNA
c. association of the 30S and the 50S ribosomal subunits
d. complementary base pairing between mRNA and DNA
complementary base pairing between mRNA and DNA
The basic structure of a nucleotide includes:
base, sugar, and phosphate
The Secondary structure of a protein includes the following elements:
alpha-helix and beta-pleated sheets
What are the 2 major components of the Tobacco Mosaic Virus?
RNA and protein
Introns are known to contain termination codons (UAA, UGA, or UAG), yet these codons do not interrupt the coding of a particular protein. Why?
Exons are spliced out of mRNA before translation
These triplets cause frameshift mutations, but not termination
More than one termination codon is needed to stop translation
Introns are removed from mRNA before translation
UAA, UGA, UAG are initiator codons, not termination codons
Introns are removed from mRNA BEFORE translation.
An intron is a section of _____
RNA that is removed during RNA processing.
How did the work of Hershey and Chase contribute to the model of DNA as the genetic material?
EXTENDED RESPONSE
Hershey & Chase designed a series of experiments to determine whether phage protein or DNA is transmitted in phage replication.
They used radioactive forms of phosphorus and sulfur to follow DNA and protein, respectively.
When new phage progeny emerged, many emitted radioactivity from 32P, demonstrating that DNA had been passed on during reproduction.
Hershey & Chase used bacteriophages to determine which material was replicated after infecting a host.
Heavy phosphorus was used to label DNA in one sample, while radioactive sulfur was used to label the protein in the other.
After infecting a host, the ghost phages were viewed to determine which label remained. The phages with labeled sulfur resulted in ghost phages with labeled sulfur, and the other sample’s had no label; indicating the material injected into the host was DNA, and therefore the genetic material.
Once transcribed, eukaryotic mRNA typically undergoes substantial alteration that includes
excision of introns
Given the figure above, is it DNA or RNA? ____ .
Is the arrow closest to the 5’ or 3’ end? _____
Spleen diesterase is an enzyme that breaks the covalent bond that connects the phosphate to the 5’ carbon.
Assume that the dinucleotide is digested with spleen diesterase.
To which base and to which carbon on the sugar is the phosphate now attached, A or T? _____. 3’ or 5’? _____
(pic of 2 rings attached to each other, top one is A, bottom is T, arrow pointing to bottom left C of bottom ring)
A
----
T
--> C
DNA
3’ end
A
3’
The genetic code is fairly consistent among all organisms.
The term often used to describe such consistency is
universal
To translate a mRNA you require two other RNAs. These are …..
tRNA and rRNA
Significant in the deciphering of the genetic code was the discovery of the enzyme Polynucleotide Phosphorylase.
What was this enzyme used for?
The manufacture of RNA for cell-free systems.
You are provided a sample of human genomic dsDNA and told that adenine makes up 34% of the nucleotides in the sample. Approximately what percentage of the nucleotides in the sample will be guanine?
8% 16% 34% 66% Given the size of the human genome, it would be impossible to determine the percentage asked for
16%
As a ribosome translocates along an mRNA molecule by one codon, which of the following occurs?
The tRNA that was in the A site moves into the P site
Explain at least two reasons why the following definition of a gene is inadequate:
“A gene consists of DNA sequences that are transcribed into a single RNA molecule that encodes a single polypeptide.”
Because a gene can encode for more than one protein; the use of word “single” is too exclusive.
Genes can be transcribed into multiple RNA molecules.
RNA molecules can encode for more than one polypeptide
Below is a list of terms, each term relating to the replication of chromosomes.
Describe the role/relationship of each in/to chromosome replication.
Okazaki fragment
Lagging strand
Bidirectional
Okazaki fragments are segments of DNA synthesized along the lagging strand, in the 5’ to 3’ direction
Lagging strand: the strand from which DNA is copied in segments due to the anti-parallel nature of DNA–the lagging strand has its 5’ end continually getting farther away from the replication fork.
Bidirectional–when DNA replication occurs in both directions, counterclockwise and clockwise, from the origin of replication of circular DNA; two replication forks
An organism has a G content of 28%. What is the percentage for A?
22
An organism has a G content of 33%.
What is the percentage for A?
17
An organism has an A + T content of 60%.
What is the percentage for C?
20
An organism has an A + T content of 52%.
What is the percentage for C?
24
Short “bursts” of DNA synthesis on the lagging strand produce ______________.
Okazaki fragments
Assume the following pathway:
Precursor —-> L —-> D —-> C—-> Product
Mutations for 3 genes (genes I, II, III) have been isolated that interrupt this pathway.
Addition of: L, D, C rescues mutations in gene III C rescues mutations in gene II D, C rescue mutations in gene I In what order do genes I, II, and III function in this pathway?
III, I, II
