Bio 313 Chapter 8
Nonhistone chromosomal proteins
(50% chromosomal proteins). These include: -- structural proteins at centromere (e.g., spindle attachment proteins) & at telomere (e.g., proteins that stabilize the chromosome) -- enzymes involved in transcription and DNA replication (e.g., DNA & RNA polymerases) -- other DNA-binding proteins (e.g., regulatory proteins such as transcription factors)
Histone
(50% of chromosomal proteins) (are not found in prokaryotes) HI, H2A, H2B, H3, H4 Contain positively- charged amino acids (arg, lys)
2;3
A base pairs with T ( __ H- bonds) C base pairs with G ( __ H- bonds)
Given that each nucleosome contains about 140 bp of DNA tightly associated with the core histone octamer, another 20 bp associated with histone H1, and 40 bp in the linker region, then one nucleosome occurs for every 200 bp of DNA. 6.4 × 109 bp divided by 2 × 102 bp/nucleosome = 3.2 × 107 nucleosomes (32 million). Each nucleosome contains two of each of the following histones: H2A, H2B, H3, and H4. A nucleosome plus one molecule of histone H1 constitute the chromatosome. Therefore, nine histone protein molecules occur for every nucleosome. 3.2 × 107 nucleosomes × 9 histones = 2.9 × 108 molecules of histones are complexed to 6.4 billion bp of DNA.
A diploid human cell contains approximately 6.4 billion base pairs of DNA. a) How many nucleosomes are present in such a cell? (Assume that the linker DNA encompasses 40 bp.) b) How many histone proteins are complexed with this DNA?
145-147; 1.6
A nucleosome "core" has _________ bp of DNA wrapped ~__X around a histone octomer (2 each of H2A, H2B, H3 and H4)
No, the student has not demonstrated that transformation has taken place. A single mutation could convert the IIR strain into the virulent IIS strain. Thus, the student cannot determine whether the conversion from IIR to IIS is due to transformation or to a mutation. Also, the student has not demonstrated that the heat was sufficient to kill all the IIS bacteria. A second useful control experiment would have been to inject the heat- killed IIS into mice and see if any of the IIS bacteria survived the heat treatment.
A student mixes some heat-killed-type IIS Streptococcus pneumoniae bacteria with live type IIR bacteria and injects the mixture into a mouse. The mouse develops pneumonia and dies. The student recovers some type IIS bacteria from the dead mouse. If this is the only experiment conducted by the student, has the student demonstrated that transformation has taken place? What other explanations might explain the presence of the type IIS bacteria in the dead mouse?
Chargaffs Rules
Amount of T = Amount of A (T/A=1) Amount of G = Amount of C (G/C=1) so (A+G)/(T+C)=1.0
chromatid
An unreplicated chromosome is also called a _______ (1 linear DNA molecule)
Took three tubes with heat killed IIIS bacteria, added RNase, protease, DNase. added to IIR bacteria. RNase= IIIS and IIR present protease= IIIS and IIR present DNase= only IIR conclusion: DNase killed DNA and nothing was transformed so DNA is the transforming principle
Avery, Macleod, and McCarty experiment:
C-1; N-9
Base attaches to ___ of sugar via _____ purines (glycosyl bond)
C-1; N-1
Base attaches to ___ of sugar via _____ pyrimidines (glycosyl bond)
No. The flow of information predicted by the central dogma is from DNA to RNA to protein. An exception to the central dogma is reverse transcription, whereby RNA encodes DNA. However, biologists currently do not know of a process in which the flow of information is from proteins to DNA, which is required by the theory of the inheritance of acquired characteristics.
Chapter 1 considered the theory of the inheritance of acquired characteristics and noted that this theory is no longer accepted. Is the central dogma consistent with the theory of the inheritance of acquired characteristics? Why or why not?
Prokaryotic chromosomes are usually circular, whereas eukaryotic chromosomes are linear. Prokaryotic chromosomes generally contain the entire genome, whereas each eukaryotic chromosome has only a portion of the genome. The eukaryotic genome is divided into multiple chromosomes. Prokaryotic chromosomes are generally much smaller than eukaryotic chromosomes and have only a single origin of DNA replication, whereas eukaryotic chromosomes contain multiple origins of DNA replication. Prokaryotic chromosomes are typically condensed into nucleoids, which have loops of DNA compacted into a dense body. Eukaryotic chromosomes contain DNA packaged into nucleosomes, which are further coiled and packaged into structures of successively higher order. The condensation state of eukaryotic chromosomes varies with the cell cycle.
Compare and contrast prokaryotic and eukaryotic chromosomes. How are they alike and how do they differ?
chromatin
DNA + associated proteins =
The phosphate backbone of DNA molecules typically carries a negative charge, thus making the DNA molecules attractive to the positive pole of the current.
DNA molecules of different sizes are often separated using a technique called electrophoresis (see Chapter 14). With this technique, DNA molecules are placed in a gel, an electrical current is applied to the gel, and the DNA molecules migrate toward the positive (+) pole of the current. What aspect of its structure causes a DNA molecule to migrate toward the positive pole?
DNA is first packaged into nucleosomes; the nucleosomes are packed to form a 30- nm fiber. The 30-nm fiber forms a series of loops that pack to form a 250 nm fiber, which in turn coils to form a 700-nm chromatid.
Describe in steps how the double helix of DNA, which is 2 nm wide, gives rise to a chromosome that is 700 nm wide.
The nucleosome core particle contains two molecules each of histones H2A, H2B, H3, and H4, which form a protein core with 145-147 bp of DNA wound around the core. A chromatosome contains the nucleosome core and a molecule of histone H1.
Describe the composition and structure of the nucleosome.
Unique-sequence DNA, present in only one or a few copies per haploid genome, represents most of the protein coding sequences, plus a great deal of sequences with unknown function. Moderately repetitive sequences, a few hundred to a few thousand base pairs long, are present in up to several thousand copies per haploid genome. Some moderately repetitive DNA consists of functional genes that code for rRNAs and tRNAs, but most is made up of transposable elements and remnants of transposable elements. Highly repetitive DNA, or satellite DNA, consists of clusters of tandem repeats of short (often less than 10 base pairs) sequences present in hundreds of thousands to millions of copies per haploid genome.
Describe the different classes of DNA sequence variation that exist in eukaryotes.
Telomeres are the stable ends of the linear chromosomes in eukaryotes. They prevent degradation by exonucleases and prevent joining of the ends. Telomeres also enable the replication of the ends of the chromosome. Telomeric DNA sequences consist of repeats of a simple sequence, usually in the form of 5′-Cn(A or T)m.
Describe the function and molecular structure of a telomere.
Took mice and injected with IIR (nonvirulent) and IIIS (virulent). IIR=alive, IIIS=dead, heat killed IIIS= alive, mix of IIR and heat killed IIIS= dead. DNA from IIIS came out of the donated protein and transformed into the IIR strain.
Griffith: The transforming principle
20-22
H1 histone clamps DNA to histone octomer; H1 binding requires _______ bp DNA beyond the 145-147 bp (this is the 167 bp nucleosome)
Most likely, the ribgrass viral genome is a single-stranded RNA. The presence of uracil indicates that the viral genome is RNA. For the molecule to be double- stranded RNA, we would predict equal percentages of adenine and uracil bases and equal percentages of guanine and cytosine bases. Neither the percentages of adenine and uracil bases nor the percentages of guanine and cytosine bases are equal, indicating that the viral genome is likely single stranded.
Heinz Shuster collected the following data on the base composition of the ribgrass virus (H. Shuster, in The Nucleic Acids: Chemistry and Biology, vol. 3, E. Chargaff and J. N. Davidson, Eds. New York: Academic Press, 1955). On the basis of this information, is the hereditary information of the ribgrass virus RNA or DNA? Is it likely to be single stranded or double stranded? Ribgrass virus: AGCTU 29.3 25.8 18.0 0.0 27.0
+; PO-4
Histone "tails" are _ charged (presence of lys and arg) and interact with the neg. charged _____ of DNA
Hershey and Chase used P-labeled phages to infect bacteria. The progeny phage released from these bacteria emitted radioactivity from 32P. The presence of the 32P in the progeny phage indicated that the infecting phages had passed DNA on to the progeny phage.
How did Hershey and Chase show that DNA is passed to new phages in phage reproduction?
DNA nucleotides, or deoxyribonucleotides, have a deoxyribose sugar that lacks an oxygen molecule at the 2′ carbon of the sugar molecule. Ribonucleotides, or RNA nucleotides, have a ribose sugar with an oxygen linked to the 2′ carbon of the sugar molecule. Ribonucleotides may contain the nitrogenous base uracil, but not thymine. DNA nucleotides contain thymine, but not uracil.
How does an RNA nucleotide differ from a DNA nucleotide?
Supercoiling arises from overwinding (positive supercoiling) or underwinding (negative supercoiling) of the DNA double helix; from a lack of free ends, as in circular DNA molecules; when the ends of the DNA molecule are bound to proteins that prevent them from rotating about each other.
How does supercoiling arise? What is the difference between positive and negative supercoiling?
1,4,6,10,11
How many of these are true about this molecule? It is____ 1. negatively supercoiled 2. a eukaryotic chromosome 3. overrotated 4. a substrate for topoisomerase 5. Z-DNA 6. closed circular 7. smiling 8. has 30 bp/ turn of the helix 9. has one centromere 10. has two polynucleotide strands 11. breathing
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%). Therefore, the percentages of each of the other bases if the thymine content is 15% are adenine = 15%; guanine = 35%; and cytosine = 35%.
If a double-stranded DNA molecule is 15% thymine, what are the percentages of all the other bases?
Tubes 1, 4, and 5. The DNA of the bacteriophage contains phosphorus and the protein contains sulfur. When the bacteriophages infect the cell, they inject their DNA into the cell, but the protein coats stay on the surface of the cell. The protein coats are sheared off in the blender, while the cells with the DNA pellet at the bottom of the tube. Thus, cells infected with 35S-labeled bacteriophage will have32 radioactivity associated with the protein coats, whereas those cells infected with P- labeled bacteriophage will have radioactivity associated with the cells.
Imagine that you are a student in Alfred Hershey and Martha Chase's laboratory in the late 1940s. You are given five test tubes containing E. coli bacteria infected with T2 bacteriophages that have been labeled with either 32P or 35S. Unfortunately, you forgot to indicate which tubes are labeled with 32P and which with 35S. You place the contents of each tube in a blender and turn it on for a few seconds to shear off the protein coats. You then centrifuge the contents to separate the protein coats and the cells, check for the presence of radioactivity, and obtain the results shown here. Which tubes contained E. coli infected with 32P-labeled phage? Explain your answer. Tube number: Radioactivity present in 1: Cells 2: Protein coats 3: Protein coats 4: Cells 5: Cells
A-DNA
It forms when water is NOT plentiful (also a right-handed helix, but is shorter and wider than B-DNA (not found in organisms)
transcription; replication
Major and minor grooves bind proteins that regulate _________ and _________; bases are exposed in the grooves, can recognize specific proteins
phosphodiester; -OH; condensation
Nucleotides connected to one another via __________ bonds between ___ groups of adjacent sugars at 3'-C & 5'-C (i.e., 2 ______________ reactions occur: removal of 2 H20)
3′—TAACGATGCC—5′
OnenucleotidestrandofDNAmoleculehasthebasesequenceillustratedbelow. 5′—ATTGCTACGG—3′ Give the base sequence and label the 5′ and 3′ ends of the complementary DNA nucleotide strand.
C-5; phosphoester
PO4 attached to ___ of sugar (___________ bond)
No, the mouse would not have contracted pneumonia and died. Although the mouse would have received IIIS DNA, which codes for virulent Streptococcus pneumoniae, there are no live bacteria for this DNA to transform. Live bacteria are required for pneumonia to develop.
Predict what would have happened if Griffith had mixed some heat-killed type IIIS bacteria and some heat-killed type IIR bacteria and injected this mixture into a mouse. Would the mouse have contracted pneumonia and died? Explain why or why not.
Although the chemical composition of the genetic material may be different from that of DNA, it more than likely will have similar properties to those of DNA. As stated in this chapter, the genetic material must contain complex information, replicate or be replicated faithfully, and encode the phenotype. Even if the material on the planet is not DNA, it must meet these criteria. Additionally, the genetic material must be stable.
Suppose that an automated, unmanned probe is sent into deep space to search for extraterrestrial life. After wandering for many light-years among the far reaches of the universe, this probe arrives on a distant planet and detects life. The chemical composition of life on this planet is completely different from that of life on Earth, and its genetic material is not composed of nucleic acids. What predictions can you make about the chemical properties of the genetic material on this planet?
grooves
The 8 histones bind to the major and minor _________ of DNA
linker
The DNA between the nucleosomes is called _______ DNA
hydroxyl (-OH) because oxygen is electronegative
The _______________ of ribose at C-2 makes RNA more reactive and less stable than DNA. why?
Several aspects contribute to the stability of the DNA molecule. The relatively strong phosphodiester linkages connect the nucleotides of a given strand of DNA. The helical nature of the double-stranded DNA molecule results in the negatively charged phosphates of each strand being arranged to the outside and away from each other. The complementary nature of the nitrogenous bases of the nucleotides helps hold the two strands of polynucleotides together. The stacking interactions of the bases, which allow for any base to follow another in a given strand, also play a major role in holding the two strands together. Finally, the ability of DNA to have local variations in secondary structure contributes to its stability. RNA nucleotides or ribonucleotides contain an extra oxygen at the 2′ carbon of the ribose sugar. This extra oxygen at each nucleotide makes RNA a less stable molecule.
The introduction to this chapter, which describes the sequencing of 4000-year-old DNA, emphasizes DNA's extreme stability. What aspects of DNA's structure contribute to the stability of the molecule? Why is RNA less stable than DNA?
how it gets all packed into chromosome
The nucleosome-containing DNA is further packaged by looping, coiling, and compression to make fibers that are further looped, coiled and compressed.......etc.
1. DNA is the "transforming principle" in the bacterium Streptococcus pneumoniae (causes pneumonia): Griffith (1928); Avery, MacLeod & McCarty (1944) 2. Hershey-Chase experiment (the "kitchen blender" experiment) (1952)
Two early, landmark findings revealed that DNA is the genetic material
polynucleotide right opposite outside; inside
Watson and Cricks model of DNA: 1. DNA is a double Helix (2 ________________ strands wind around each other 2. Is an α-helix (________-handed) 3. Strands run in _________ directions; strands have a 5' end and a 3' end 4. Sugar-phosphates are on the __________ of helix, bases are on __________
B-DNA; water
Watson and crick helix= _______ forms a right-handed helix (clockwise spiral) and there are 10 base pairs per helix turn (3.4 nm/turn). * when _____ is plentiful
1962; died of ovarian cancer
Watson, Crick & Wilkins shared Nobel Prize for Medicine (______) why not franklin?
Euchromatin undergoes regular cycles of condensation during mitosis and decondensation during interphase, whereas heterochromatin remains highly condensed throughout the cell cycle, except transiently during replication. Nearly all transcription takes place in euchromatic regions, with little or no transcription of heterochromatin.
What are some differences between euchromatin and heterochromatin?
the structure of DNA gives insight into the three fundamental genetic processes. The Watson and Crick model suggests that the genetic information or instructions are encoded in the nucleotide sequences. The complementary polynucleotide strands indicate how faithful replication of the genetic material is possible. Finally, the arrangement of the nucleotides is such that they specify the primary structure or amino acid sequence of protein molecules.
What are some of the important genetic implications of the DNA structure?
Replication, transcription, and translation are the components of the central dogma of molecular biology.
What are the three major pathways of information flow within the cell?
Cytosine, Thymine, Uracil
What are the three pyrimidines?
Adenine and Guanine
What are the two purines?
(1) The genetic material must contain complex information. (2) The genetic material must replicate or be replicated faithfully. (3) The genetic material must have the capacity to vary or mutate to generate diversity. (4) The genetic material must encode the phenotype or have the ability to code for traits.
What four general characteristics must the genetic material possess?
Supercoiling compacts the DNA. Negative supercoiling helps to unwind the DNA duplex for replication and transcription.
What functions does supercoiling serve for the cell?
Transformation occurs when a transforming material (or DNA) genetically alters the bacterium that absorbs the transforming material. Avery and his colleagues demonstrated that DNA is the transforming material by using enzymes that destroyed the different classes of biological molecules. Enzymes that destroyed proteins or nucleic acids had no effect on the activity of the transforming material. However, enzymes that destroyed DNA eliminated the biological activity of the transforming material. Avery and his colleagues were also able to isolate the transforming material and demonstrate that it had chemical properties similar to DNA.
What is transformation? How did Avery and his colleagues demonstrate that the transforming principle is DNA?
DNA replication, transcription, and translation.
Which of the processes of information transfer illustrated in Figure 8.14 are required for the T2 phage reproduction illustrated in Figure 8.4?
Griffith
Who Demonstrated that heat-killed material from bacteria could genetically transform live bacteria.
Kossel
Who Determined that DNA contains nitrogenous bases.
Miescher
Who Determined that DNA is acidic and high in phosphorus. German 1860's, chemistry of pus
Avery, Macleod, and McCarty
Who Determined that DNA is responsible for transformation in bacteria.
Chargaff
Who Discovered regularity in the ratios of different bases in DNA. Was testing tetra nucleotide theory, by measuring amounts of different bases in different organisms. Proved they were different which meant DNA has informational complexity.
Levene; complexity for the instructions to an entire organism
Who Discovered that DNA consists of repeating nucleotides. (tetra nucleotide theory) If it were the same repeating nucleotides though what wouldn't be possible?
Hershey and Chase
Who Identified DNA as the genetic material in bacteriophage.
Franklin and Wilkins
Who Took X-ray diffraction pictures used in determining the structure of DNA.
Watson and Crick
Who Worked out the helical structure of DNA by correctly interpreting data of Wilkins and Franklin and building models.
Secondary
__________ structure: 3-D structure (this is the double helix)
Primary
__________ structure: linear sequence of covalently- linked nucleotides (called a polynucleotide strand)
tertiary
__________ structure: packing arrangements of the double helix in the chromosome
nucleosomes
____________ are the "repeating unit" of chromatin ("beads-on-a-string")
competence
ability of a cell to take up DNA from the environment (ability to be transformed)
sister chromatids
after DNA synthesis, the chromosome contains 2 ________ __________ (2 identical, linear DNAs, held together by the centromere)
allele
alternate form of a gene; resides at the same place on each chromosome
Centromeres
attachment site for spindle microtubules via the kinetochore; composed of heterochromatin
telomeres
chromosome ends; composed of heterochromatin
8
histone octomer has _ subunits
enzymes
involved in transcription and DNA replication (e.g., DNA & RNA polymerases)
oligomer
macromolecular complex composed of subunits (usually proteins) that are most often bonded to one another non-covalently ex: Number of subunits (Greek): monomer, dimer, trimer, tetramer, pentamer, hexamer, septamer, octomer
transformation
mechanism by which DNA in the medium is taken up by the cell
Deoxyadenosine 5'-monophosphate (dAMP) OH on 2'
name and whats the difference for a ribo?
Deoxycytidine 5'-monophosphate (dCMP) OH on 2'
name and whats the difference for a ribo?
Deoxyguanosine 5'-monophosphate (dGMP) OH on 2'
name and whats the difference for a ribo?
Deoxythymidine 5'-monophosphate (dTMP) OH on 2'
name and whats the difference for a ribo?
homologous pair of chromosomes
one chromosome came from the mother, the other from the father; both chromosomes have the same structure and the same genes in the same order
structural
proteins at centromere (e.g., spindle attachment proteins) & at telomere (e.g., proteins that stabilize the chromosome)
Origins of replication (ori)
sites where DNA synthesis (replication) begins; many origins per chromosome, hence found in euchromatin and heterochromatin
1)DNA can exist in a condensed (compacted) state or a decondensed (extended) state; there is a continuum of condensation Packing is dynamic : a given region of DNA can change from one state to the other 2)Eukaryotic DNA is associated with many proteins (qualitatively and quantitatively) 3) two classes of proteins: histones and non histones 4)nucleosomes are repeating unit of chromatin 5)H1 histone clamps DNA to octomer 6)The nucleosome-containing DNA is further packaged by looping, coiling, and compression to make fibers that are further looped, coiled and compressed.......etc.
six points of Eukaryotic chromosome packing
recombination
takes place between the foreign DNA and the host chromosome (called recombinant DNA)
euchromatin
what Type of chromatin: undergoes dynamic packing; nearly all genes are in euchromatin; hence, this is where transcription occurs
heterochromatin
what type of chromatin: highly condensed; present in centromeres, telomeres; inactivated X (female mammals); most of Y; very little transcription occurs in heterochromatin
