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Final

BIOL 308 Final: 308studyquestions

36 Pages
76 Views
Fall 2016

Department
Biology
Course Code
BIOL308
Professor
Dragana Miskovic
Study Guide
Final

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LECTURES 1-4
1. What information could you obtain from a genetic approach of studying mutants defective in a particular
process?
-the potential function and “importance” of the protein  identification/isolation/survival of mutants
-how many genes are involved in a certain process
-order of these genes (proteins) in the process by applying genetic approach (complementation analysis)
-interaction between different genes (proteins) by using genetic approach (genetic suppression)
2. How would you define permissive conditions in respect to temperature sensitive mutants?
-permissive conditions are the temperatures at which the mutants can survive and grow
3. Define (or compare and contrast): a) gene expression; transcription; replication; translation; b) gene; allele
a) -Gene Expression: the processes through which the information carried by a gene is converted into an observable product
(either RNA or protein)
-Transcription: the process of copying DNA to RNA by enzymatic processes
-Replication: the process of copying a double stranded DNA molecule (DNA synthesis)
-Translation: the process that converts an mRNA sequence into a chain of amino acids that form a protein
b) -Gene: the functional unit of heredity; the entire DNA sequence necessary for the synthesis of a RNA molecule or functional
polypeptide (it includes coding and regulatory regions)
-Allele: different version of the same gene
4. Explain by using your own words the meaning/significance of gene expression.
-gene expression is the conversion of a sequence of DNA into a final observable product (either RNA or protein)
-it is important since all living things rely on proteins to function and survive  everything in/about the living cell/organism is
about proteins
5. What are the roles of model organisms in molecular biology studies? Choose two model organisms and explain
your reasoning.
-model organisms help us understand (at a basic molecular level) how something affects/alters cells and the organism in general;
can be extrapolated to more complex organisms
Escherichia coli Drosophila
-short reproductive period
-simple
-relatively cheap
-easy to maintain
-lots of data available
-4 million bp
-4000 different proteins
-divides every 20-60 minutes
-simple nutritional requirement
-useful for genetic experiments
-developmental studies  body plan formation
-relatively small
-cheap
-easy to maintain
-lots of data available
-first to be extrapolated to higher mammals
6. What are three main functions of DNA? Explain the importance of each of them.
-stores information – sequence of bases codes for proteins, RNAs, regulatory signal
-replicates faithfully – semiconservative replication is basis of reproduction and cell growth
-ability to mutate – basis of evolution and allelic variation
7. What is (are) the role(s) of phosphodiester bonds in DNA structure? What is (are) the role(s) of hydrogen bonds
in DNA structure? What is (are) the role(s) of hydrophobic interactions in DNA structure?
-phospho-diester bonds contain a negative charge  thus, the backbone contains a negative charge that repels two different
strands from each other; rigid covalent bonds that are basis of structure
-hydrogen bonds keep the two strands held together – complementary base pairing
-the hydrophobic interaction helps stabilize the molecule since it forces the nitrogenous bases together and keeps the two
negatively charged backbones apart
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8. What noncovalent interactions are involved in maintaining the
double-helical conformation of DNA?
-Van der Waals interactions
-Hydrophobic interactions
-Ionic interactions
-Hydrogen bonding
9. Learn to recognize nitrogenous bases (A,T,G,C,U).
10.Describe Meselson-Stahl experiment and explain how it showed that DNA replication is semiconservative?
-E. coli cells were grown on media containing 15N for several generations  this made the DNA molecules denser than normal 
cells were then grown for two generations on 14N  if the DNA got degraded, then the newly synthesized DNA would contain one
hybrid band between the two nitrogen densities  since two different bands resulted, it confirmed that DNA replicates semi-
conservatively  two strands of a parental DNA separate and each serves as a template for synthesis of a new daughter strand by
complementary base pairing
11.What is meant by saying that a DNA strand has polarity? That two strands of DNA are antiparallel? That the
strands are complementary to one another?
-5’ (phosphate)  3’ (hydroxyl)
-at either end of the helix, the 5’ end of one strand will pair up with the 3’ end of another strand
-the base pairs form hydrogen bonds with each other, such that A will always associate with T and C will always associate with G
 complementary bases
12.If a C content of a preparation of double-stranded DNA is 20%, what is the T content?
-T content = 30%
13.What is the difference between nucleoside and nucleotide?
-nucleoside = sugar + nitrogenous base
-nucleotide = sugar + nitrogenous base + phosphate group
14.Describe the conformational characteristics of B DNA (or A DNA, Z DNA, triple-helical DNA). When does this (any
of the above) form of DNA occur?
B DNA A DNA Z DNA Triple Helical DNA
- ~10 base pairs per turn
-turn is every 3.4nm
-bases are perpendicular
to helix axis
-right handed DNA
-most in vivo DNA
-11 pairs per turn
-turn every 2.8 nm
-bases exhibit tilt with
respect to helix axis (20º)
-right handed DNA
-found in low water
content
-DNA-RNA and RNA-RNA
helices in test tube
-also found locally and
temporarily in vivo
-12 base pairs per
turn
-turn every 4.5 nm
-tilt 7º
-left handed
-found in very high
salt concentrations
-found in d(CG)
polymers
-formed when purines
make one strand and
pyrimidines the other
(allows for third strand
accommodations)
-maybe in vivo during
DNA recombination or
repair
15.How does high salt concentration influence denaturation kinetics of DNA? Explain your reasoning.
-high salt concentrations (positive ions) impede denaturation, since these positive ions help to stabilize the DNA phosphodiester
backbone  low salt concentrations reduce the stabilization and thus promotes denaturation of double stranded DNA
16.What are the classes of DNA sequences in genomic DNA?
-slow (unique): coding sequences  one to few copies, have lots of difficulty finding each other during renaturation (slow
renaturation)
-middle (moderately repetitive): gene families  moderate #, find each other with relative ease, need more time (middle
renaturation)
-fast (highly repetitive): short repeats of bp, no apparent function  lots of them and they are able to find each other really easily
(fast renaturation)
17.What is Cot analysis?
-Cot measures the rate of renaturation, which is a measure of the complexity of the DNA/genome  simple sequences renature
more quickly than complex sequences
18.Who received a Nobel Prize for 3D DNA structure?
-James Watson, Francis Crick, and Maurice Wilkins (not Rosalind Franklin)
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19.If you had two solutions of DNA, one single-stranded and one double-stranded, with equivalent absorbance at
260 nm, how would the concentrations of DNA compare in these two solutions?
-in single stranded DNA, the bases are unstacked and absorbance increases (hyperchromic effect)
-in double stranded DNA, the bases are stacked and absorbance is reduced (hypochromic effect)
-thus, to have equivalent absorbances, the concentration of double stranded DNA must be high, while the concentration of single
stranded DNA must be low
LECTURES 5-7
1. Thinking question re DNA/RNA structure: Certain chemical agents acting on DNA could convert cytosine to
uracil through the process of deamination (chopping off the amino group). This mutation is routinely repaired
by the existing repair mechanism (uracil is removed and it gets replaced by cytosine). Knowing this, how would
you explain why DNA contains thymine and NOT uracil.
-it is important that DNA uses thymine because if uracil was used, the repair mechanism wouldn’t be able to differentiate between
mutated cytosine and actual uracil that is important to the sequence of bases
2. How does complexity of bacterial genome differ from that of eukaryotic (calf) genome?
-E. coli genome has no repetitive sequences  whole genome is one unique sequence
-calf genome has lots of repetitive sequences  its unique sequences are more complex than E. coli however
3. Explain C value paradox.
-no correlation between the amount of DNA and the apparent complexity of organisms  prokaryotic genomes contain only non-
repetitive DNA
4. List and briefly explain factors that influence DNA renaturation kinetics.
-DNA concentration  greater [DNA], greater chance of faster renaturation
-salt concentration  ionic conditions mask the repulsion forces of phosphate backbone
-temperature  melting temperature = temp. at which 50% of DNA is denatured  high temperatures denature DNA
-time
-size of DNA fragment  bigger the DNA fragment, more difficult is renaturation
-complexity  simple sequences renature faster than complex sequences
5. You have found a new species of insects. To evaluate the complexity of the genome of this species, you isolate
genomic DNA from, fragment the DNA to uniform 500 base pair pieces, denature the DNA and measure the rate
of reassociation. Your data is represented in the curve below (sorry for the bad drawing):
(a) How many classes of DNA (in respect to sequence complexity) are found in this organism?
-3 classes
(b) What can you say about the relative complexity of each class? What fraction of the genome falls into each
class?
-fast  not complex at all, very repetitive (25%)
-medium  somewhat complex (25%)
-slow  very complex (50%)
6. List three (3) differences between prokaryotic Topoisomerase I and Gyrase.
-Topoisomerase I relaxes negative supercoils; gyrase introduces negative supercoils
-Gyrase is a topoisomerase II, cuts double stranded DNA; topoisomerase I cuts one strand
-Topoisomerase I changes L in steps of 1, gyrase changes L in steps of 2
7. What are topological isomers of DNA?
-DNA differing only in their states of supercoiling
8. Explain the importance of DNA supercoiling for the cell survival?
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Description
LECTURES 14 1. What information could you obtain from a genetic approach of studying mutants defective in a particular process? the potential function and importance of the protein identificationisolationsurvival of mutants how many genes are involved in a certain process order of these genes (proteins) in the process by applying genetic approach (complementation analysis) interaction between different genes (proteins) by using genetic approach (genetic suppression) 2. How would you define permissive conditions in respect to temperature sensitive mutants? permissive conditions are the temperatures at which the mutants can survive and grow 3. Define (or compare and contrast): a) gene expression; transcription; replication; translation; b) gene; allele a) Gene Expression: the processes through which the information carried by a gene is converted into an observable product (either RNA or protein) Transcription: the process of copying DNA to RNA by enzymatic processes Replication: the process of copying a double stranded DNA molecule (DNA synthesis) Translation: the process that converts an mRNA sequence into a chain of amino acids that form a protein b) Gene: the functional unit of heredity; the entire DNA sequence necessary for the synthesis of a RNA molecule or functional polypeptide (it includes coding and regulatory regions) Allele: different version of the same gene 4. Explain by using your own words the meaningsignificance of gene expression. gene expression is the conversion of a sequence of DNA into a final observable product (either RNA or protein) it is important since all living things rely on proteins to function and survive everything inabout the living cellorganism is about proteins 5. What are the roles of model organisms in molecular biology studies? Choose two model organisms and explain your reasoning. model organisms help us understand (at a basic molecular level) how something affectsalters cells and the organism in general; can be extrapolated to more complex organisms Escherichia coli Drosophila short reproductive period useful for genetic experiments simple developmental studies body plan formation relatively cheap relatively small easy to maintain cheap lots of data available easy to maintain 4 million bp lots of data available 4000 different proteins first to be extrapolated to higher mammals divides every 2060 minutes simple nutritional requirement 6. What are three main functions of DNA? Explain the importance of each of them. stores information sequence of bases codes for proteins, RNAs, regulatory signal replicates faithfully semiconservative replication is basis of reproduction and cell growth ability to mutate basis of evolution and allelic variation 7. What is (are) the role(s) of phosphodiester bonds in DNA structure? What is (are) the role(s) of hydrogen bonds in DNA structure? What is (are) the role(s) of hydrophobic interactions in DNA structure? phosphodiester bonds contain a negative charge thus, the backbone contains a negative charge that repels two different strands from each other; rigid covalent bonds that are basis of structure hydrogen bonds keep the two strands held together complementary base pairing the hydrophobic interaction helps stabilize the molecule since it forces the nitrogenous bases together and keeps the two negatively charged backbones apart
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