What three general characteristics must the genetic material possess?
1) Must contain complex info that encodes the phenotype
2) Must replicate or be replicated faithfully
3) Must be able to mutate to generate diversity
How does an RNA nucleotide differ from a DNA nucleotide?
DNA nucleotides = Lacks O on 2' Carbon of Sugar, Thymine
RNA nucleotides = Has O on 2' Carbon of Sugar, Uracil
How does a purine differ from a pyrimidine? What purines and pyrimidines are found in DNA and RNA?
Purine - six sided ring attached to five sided ring
Pyrimidine - one six sided ring
DNA - Purines = AG Pyrimidines = TC
RNA - Purines = AG Pyrimidines = UC
Which bases are capable of forming hydrogen bonds with each other.
A - T 2
C - G 3
For each organism, compute the ratio of (A + G)/(T + C) and the ratio of (A + T)/(C + G).
Organism and tissue A-G-C-T
Sheep thymus 29.3-21.4-21.0-28.3
Pig liver 29.4-20.5-20.5-29.7
Human thymus 30.9-19.9-19.8-29.4
Human sperm 30.9-19.1-18.4-31.6
Salmon sp
Sheep Thymus 1.03 and 1.36
Pig Liver 0.99 and 1.44
Human Thymus 1.03 and 1.36
Human Sperm 1.00 and 1.67
Salmon Sperm 1.02 and 1.43
Herring Sperm 1.04 and 1.29
b. Are these ratios constant or do they vary among the organisms? Explain why.
The ratios for th
Which of the following relations will be found in the percentages of bases of a double-stranded DNA molecule?
A double-stranded DNA molecule will contain equal percentages of A and T nucleotides and equal percentages of G and C nucleotides. The combined percentage of A and T bases added to the combined percentage of the G and C bases should equal 100.
ie. A + T =
If a double-stranded DNA molecule has 15% thymine, what are the percentages of all the other bases?
The percentage of thymine (15%) should be approximately equal to the percentage of adenine (15%). The remaining percentage of DNA bases will consist of cytosine and guanine bases (100% - 15% - 15% = 70%); these should be in equal amounts (70%/2 = 35%). Th
Describe the composition and structure of the nucleosome. How do core particles differ from chromatosomes?
Nucleosome core particle = 2 moles of each histone H2A, H2b, H3, and H4 which form a protein core with 145-147 bp of DNA wound around the core.
Chromatosomes contain the nucleosome core with a molecule of histone H1.
Describe in steps how the double helix of DNA, which is 2 nm in width, gives rise to a chromosome that is 700 nm in width.
DNA - > Nucleosomes
Nucleosomes - > 30nm fiber
30nm fiber - > 250nm fiber
250nm fiber - > 700nm chromatid
What is the difference between euchromatin and heterochromatin?
Euchromatin undergoes regular cycles of condensation during mitosis and decondensation during interphase.
Heterochromatin remains highly condensed throughout the cell cycle, except transiently during replication.
Nearly all transcription takes place in eu
How did Meselson and Stahl demonstrate that replication in E. coli takes place in a semiconservative manner?
15N was incorporated in the DNA of E. coli cells
These cells were switched into a 14N medium
Samples removed at each generation
Centrifuging separate them by weight over generations
Eventually created only 2 bands
Semiconservative
What similarities and differences exist in the enzymatic activities of DNA polymerases I, II, and III? What is the function of each type of DNA polymerase in bacterial cells?
All 3 have 5' to 3' polymerase activity.
Only DNA Poly I has 3' to 5' exonuclease activity as well.
DNA Poly I - Proofreading. Removes and replaces RNA primers
DNA Poly II - DNA repair polymerase. Restarts replication after DNA dmg has halted replication.
Why is primase required for replication?
Primase is a DNA-dependent RNA polymerase.
Primase synthesizes the short RNA molecules, or primers, that have a free 3'-OH to which DNA polymerase can attach deoxyribonucleotides in replication initiation.
The DNA polymerases require a free 3'-OH to which
How does replication licensing ensure that DNA is replicated only once at each origin per cell cycle?
Only replication origins to which replication licensing factor (RPF) has bound can undergo initiation. Shortly after the completion of mitosis, RPF binds the origin during G1 and is removed by the replication machinery during S phase.
In what ways is eukaryotic replication similar to bacterial replication, and in what ways is it different?
Same:
Semiconservative
Origin serves as starting point
Primers provide 3-OH' for polymerases to begin synth
Synth is 5'-3'
Template strand is read in 3' to 5' direction
Deoxyribonucleoside triphosphates are substrates
Continuous on leading and discontinuo
What is the end-of-chromosome problem for replication? Why, in the absence of telomerase, do the ends of chromosomes get progressively shorter each time the DNA is replicated?
For DNA polymerases to work, they need the presence of a 3' OH group to which to add a nucleotide. At the ends of the chromosomes when the RNA primer is removed, there is no adjacent 3' OH group to which to add a nucleotide, thus no nucleotides are added
Outline in words and pictures how telomeres at the end of eukaryotic chromosomes are replicated.
Telomeres are replicated by the enzyme telomerase. Telomerase, a ribonucleoprotein, consists of protein and an RNA molecule that is complementary to the 3' end of the DNA of a eukaryotic chromosome. The RNA molecule also serves as a template for the addit
Phosphorous is required to synthesize the deoxyribonucleoside triphosphates used in DNA replication. A geneticist grows some E. coli in a medium containing nonradioactive phosphorous for many generations. A sample of the bacteria is then transferred to a
In the initial sample removed immediately after transfer, no 32P should be incorporated into the DNA because replication in the medium containing 32P has not yet occurred. After one round of replication in the 32P containing medium, one strand of each new
A circular molecule of DNA contains 1 million base pairs. If DNA synthesis at a replication fork occurs at a rate of 100,000 nucleotides per minute, how long will theta replication require to completely replicate the molecule, assuming that theta replicat
In bidirectional replication there are two replication forks, each proceeding at a rate of 100,000 nucleotides per minute. Therefore, it would require 5 minutes for the circular DNA molecule to be replicated by bidirectional replication because each fork
A bacterium synthesizes DNA at each replication fork at a rate of 1000 nucleotides per second. If this bacterium completely replicates its circular chromosome by theta replication in 30 minutes, how many base pairs of DNA will its chromosome contain?
Each replication complex is synthesizing DNA at each fork at a rate of 1000 nucleotides per second. So for each second, 2000 nucleotides are being synthesized by both forks (1000 nucleotides / second � 2 forks = 2000 nucleotides / second) or 120,000 nucle
How would DNA replication be affected in a cell that is lacking topoisomerase?
Topoisomerase II or gyrase reduces the positive supercoiling or torsional strain that develops ahead of the replication fork due to the unwinding of the double helix. If the topoisomerase activity was lacking, then the torsional strain would continue to i
If the gene for primase were mutated so that no functional primase was produced, what would be effect on theta replication? On rolling-circle replication?
Primase is required for replication initiation in theta form replication. If primase is nonfunctional then replication initiation would not take place resulting in no replication occurring. Rolling-circle replication does not require primase. A single-str
How is the structure of RNA similar to that of DNA? How is it different?
RNA - ribose sugar, uracil, single stranded
DNA- deoxyribose sugar, thymine, double stranded
Why is DNA more stable than RNA?
2' OH in ribose of RNA is more susceptible to degradation under alkaline conditions.
What parts of DNA make up a transcription unit?
Promoter | Transcription start site | Terminator
RNA coding region includes Transcription start site and terminator
What is the substrate for RNA synthesis? How is this substrate modified and joined together to produce an RNA molecule?
4 ribonucleoside triphosphates:
adenosine triphosphate
guanosine triphosphate
cytosine triphosphate
uridine monophosphate
Enzyme RNA Polymerase uses DNA polynucleotide strand as a template to synth a complementary RNA strand.
Nucleotides added to RNA one
Give the names of the three RNA polymerases found in eukaryotic cells and the types of RNA they transcribe.
RNA Pol I - transcribes rRNA
RNA Pol II - transcribes pre-mRNA, snoRNAs, and some miRNAs and snRNAs
RNA Pol III - transcribes small RNA molecules such as 5S rRNA, tRNAs, and some snRNAs and miRNAs
RNA Pol IV - transcribes siRNAs in plants
What are the three basic stages of transcription? Describe what happens at each stage.
Initiation: Transcription proteins assemble at the promoter to form the basal transcription apparatus and begin synthesis of RNA
Elongation: RNA polymerase moves along the DNA template in a 3' to 5' direction, unwinding the DNA and synthing the RNA in a 5
How is the process of transcription in eukaryotic cells different from that in bacterial cells?
Eukaryotic transcription requires the action of three RNA polymerases. Each type of polymerase recognizes and transcribes from different types of promoters. Binding to the promoter and initiation from the promoter requires the action of many protein trans
Compare and contrast transcription and replication. How are these processes similar and how are they different?
Same:
Utilize DNA template
Synth molecules 5' to 3'
Synth molecules antiparallel and complementary to template
Use nucleotide triphosphates as substrates
Involve complexes of proteins and enzymes necessary for catalysis
ONLY REPLICATION:
Bidirectional syn
How are the processes of transcription in archaeans and eukaryotes different? How are they similar?
A comparison of transcription between eukaryotes and archaea shows that transcription in eukaryotes shares more similarities with archaeal transcription than they do with transcription in bacteria.
1) Organisms in domain archaea use a single RNA pol for t
An RNA molecule has the following percentages of bases: A = 23%, U = 42%,
C = 21%, G = 14%.
a. Is this RNA single-stranded or double-stranded? How can you tell?
b. What would be the percentages of bases in the template strand of the DNA that contains the
a) The RNA molecule is likely to be single-stranded. If the molecule was double-stranded, we would expect nearly equal percentages of adenine and uracil, as well as equal percentages of guanine and cytosine. In this RNA molecule, the percentages of these
The following diagram represents DNA that is part of the RNA-coding sequence of a transcription unit. The bottom strand is the template strand. Give the sequence found on the RNA molecule transcribed from this DNA and label the 5? and 3? ends of the RNA.
The RNA molecule would be complementary to the template strand, contain uracil, and be synthesized in an antiparallel fashion. The sequence would be:
5?-A U A G G C G A U G C C A-3?.
The RNA strand contains the same sequence as the nontemplate DNA strand
The following sequence of nucleotides is found in a single-stranded DNA template:
A T T G C C A G A T C A T C C C A A T A G A T
Assume that RNA polymerase proceeds along this template from left to right.
a. Which end of the DNA template is 5? and which en
a) RNA is synthesized in a 5? to 3? direction by RNA polymerase, which reads the DNA template in a 3? to 5? direction. So, if the polymerase is moving from left to right on the template then the 3? end must be on the left and the 5? end on the right.
3?-A
RNA polymerases carry out transcription at a much slower rate than DNA polymerases carry out replication. Why is speed more important in replication than in transcription?
DNA polymerases are required to replicate much larger regions of DNA, such as entire chromosomes. Speed is essential to complete the replication process in a timely manner. RNA polymerases typically transcribe only small areas of the chromosomes. The spee
Most RNA molecules have three phosphates at their 5? end, but DNA molecules never do. Explain this difference.
During initiation of DNA replication, DNA nucleoside triphosphates must be attached to a 3?-OH of a RNA molecule by DNA polymerase. This process removes the terminal two phosphates of the nucleotides. If the RNA molecule is subsequently removed, then a si
The following diagram represents a transcription unit in a hypothetical DNA molecule:
5?...TTGACA...TATAAT...3?
3?...AACTGT...ATATTA...5?
a. On the basis of the information given, is this DNA from a bacterium or from a eukaryotic organism?
b. If this DNA
a) The DNA is from a bacterium as evidenced by the TATAAT sequence that corresponds to the -10 consensus sequence of a bacterial promoter and the TTGACA sequence that is identical to the -35 consensus sequence of a bacterial promoter.
b) 5?...TTGACA...TAT
What is the function of the Shine-Dalgarno consensus sequence?
The Shine-Dalgarno consensus sequence functions as the ribosome-binding site on the mRNA molecule.
a. What is the 5? cap?
b. How is the 5? cap added to eukaryotic pre-mRNA?
c. What is the function of the 5? cap?
a) The 5? end of eukaryotic mRNA is modified by the addition of the 5? cap. The cap consists of an extra guanine nucleotide linked 5? to 5? to the mRNA molecule. This nucleotide is methylated at position 7 of the base. The ribose sugars of adjacent bases
How is the poly(A) tail added to pre-mRNA? What is the purpose of the poly(A) tail?
Initially, a complex consisting of several proteins forms on the 3? UTR of the pre-mRNA molecule. Cleavage and polyadenylation specificity factor (CPSF) bind to the AAUAAA consensus sequence, which is located upstream of the 3? cleavage site. Another prot
What makes up the spliceosome? What is the function of the spliceosome?
The spliceosome consists of five small ribonucleoproteins (snRNPs). Each snRNP is composed of multiple proteins and a single small nuclear RNA molecule or snRNA. The snRNPs are identified by which snRNA (U1, U2, U3, U4, U5, or U6) each contains. Splicing
Explain the process of pre-mRNA splicing in nuclear genes.
Removal of an intron from the pre-mRNA requires the assembly of the spliceosome complex on the pre-mRNA, cleavage at both the 5? and 3? splice sites of the intron, and two transesterification reactions ultimately leading to the joining of the two exons. I
Summarize the different types of processing that can take place in pre-mRNA.
(1)
Addition of the 5? 7-mG cap to the 5? end of the pre-mRNA
(2)
Cleavage of the 3? end of a site downstream of the AAUAAA consensus sequence of the last exon
(3)
Addition of the poly(A) tail to the 3? end of the mRNA immediately following cleavage
(4)
R
How do the mRNAs of bacterial cells and the pre-mRNAs of eukaryotic cells differ? How do the mature mRNAs of bacterial and eukaryotic cells differ?
Bacterial mRNA is translated immediately upon being transcribed. Eukaryotic pre-mRNA must be processed. Bacterial mRNA and eukaryotic pre-mRNA have similarities in structure. Each has a 5? untranslated region as well as a 3? untranslated region. Both also
Identify the following items and, for each item, give a brief description of its function.
a. 5 untranslated region
b. promoter
c. AAUAAA consensus sequence
d. Transcription start site
e. 3 untranslated region
f. introns
g. exons
h. Poly(A)tail
i. 5' cap
a. 5? untranslated region
The 5? untranslated region lies upstream of the translation start site. In bacteria, the ribosome binding site or Shine-Dalgarno sequence is found within the 5? untranslated region. However, eukaryotic mRNA does not have the equi
Suppose that a mutation occurs in an intron of a gene encoding a protein. What will the most likely effect of the mutation be on the amino acid sequence of that protein? Explain your answer.
Because introns are removed prior to translation, an intron mutation would have little effect on a protein's amino acid sequence unless the mutation occurred within the 5? splice site, the 3? splice site, or the branch point. If mutations within these seq
How is biological evolution defined?
Biological evolution is change in the genetic composition of a population over time.
What are the two steps in the process of evolution?
First, mutation causes genetic variation in a population and recombination creates new combinations of genetic variants. Second, the frequencies of the variants change over time (from generation to generation), as a result of random processes (e.g., drift
What is the biological species concept? What are some of the problems with it?
The biological species concept defines species as a group of individuals that can potentially interbreed with each other but are reproductively isolated from members of other species. One obvious problem is applying this concept to asexually reproducing o
What is the difference between prezygotic and postzygotic reproductive isolating mechanisms. List the different types of each.
Prezygotic mechanisms operate before fertilization of the egg by sperm (or fusion of gametes), and postzygotic mechanisms operate after fertilization. Prezygotic mechanisms include ecological isolation, behavioral isolation, temporal isolation, mechanical
What is the basic difference between allopatric and sympatric modes of speciation?
Allopatric speciation involves populations separated by a geographic barrier that precludes gene flow between the populations. Sympatric speciation takes place between populations occupying the same geographical area.
Briefly outline the process of allopatric speciation.
First, a population is split by a geographical barrier that prevents gene flow between the two groups on either side of the barrier. The two groups then evolve independently; they accumulate genetic differences through various evolutionary processes such
What is the molecular clock?
The molecular clock is the concept (hypothesis) that the rate at which nucleotide changes take place in a DNA sequence is relatively constant over long periods of time, and therefore the number of nucleotide substitutions that have taken place between two