Unit 3 (Week 8 Nucleic Acid Structure DNA Replication and Chromosome Structure) Flashcards
What carries the genetic instructions for living things and, for example, enables a fertilized egg to develop into an embryo and eventually into an adult organism?
DNA
What provides the blueprint to create specific enzymes for the digestion of certain foods?
DNA
What are the four key criteria for something to be genetic material?
Information - The genetic material must contain the information necessary to construct an entire organism.
Replication - The genetic material must be accurately copied, a process known as replication.
Transmission - After it is replicated, the genetic material can be passed from parent to offspring. It also must be passed from cell to cell during the process of cell division.
Variation - Differences in the genetic material must account for the known variation within each species and among different species.
What is a discrete unit of genetic material composed of DNA and associated proteins?
Chromosomes. Eukaryotes have chromosomes in their cell nuclei and in plastids and mitochondria.
Greek from chromo and soma meaning colored body, refers to the early observation by microscopists that chromosomes are easily stained by colored dyes.
What is a discrete unit of genetic material composed of DNA and associated proteins?
Chromosomes. Eukaryotes have chromosomes in their cell nuclei and in plastids and mitochondria.
Greek from chromo and soma meaning colored body, refers to the early observation by microscopists that chromosomes are easily stained by colored dyes.
In the late 1920s, an English microbiologist, Frederick Griffith, studied what type of bacteria and injected mice with two strains: Type S for smooth and Type R for rough?
Pneumococci or Streptococcus pneimoniae.
What is a type of gene transfer between bacteria in which a segment of DNA from the environment is taken up by a competent cell and incorporated into the bacterial chromosome?
This was shown to happen with strep in mice.
Transformation.
How did Avery, MacLeod, and McCarty, in their experiment, prove that DNA from S type strep was responsible for transforming R type strep into S type strep?
They purified samples of DNA from S type strep, added them to mixtures of R Type bacteria and then added different enzymes such as DNase, RNase, and proteases to different mixtures to essentially denature their respective substrates. Once this was complete, and an antibody was added to remove any non-transformed R type strep, the results were centrifuged, causing all non transformed R type strep to form a pellet at the bottom.
The resulting S type was left over in each of the test tubes. The only test tube to remain “rough” was the one with DNase. This means that DNA of S type was the transforming principle in this experiment.
What is an enzyme that digests DNA?
DNase
What is an enzyme that digests RNA?
RNase
What is an enzyme that cuts proteins into smaller polypeptides?
Proteases
Explain the characteristics of the S. pneumoniae strains that made them particularly well suited for the researchers’ experiment.
Previous studies had indicated that mixing different strains could lead to transformation, or the changing of a strain into a different one. Griffith had shown that mixing heat-killed type S with living type R bacteria would result in the transformation of the type R to type S. Though mutations could cause a change of identity of certain strains, the type R to type S transformation was not due to mutation but was more likely due to the transmission of a biochemical substance between the two strains. Griffith recognized this and referred to the biochemical substance as the “transformation principle.” If Avery, MacCleod, and McCarty could determine the biochemical identity of this “transformation principle,” they could identify the genetic material for the bacteria.
What is a DNA extract?
A DNA extract contains DNA that has been purified from a sample of cells.
In the experiment of Avery, MacLeod, and McCarty, what was the purpose of using protease, RNase, and DNase if only the DNA extract caused transformation?
The researchers could not verify that the DNA extract was completely pure, that is, lacking small amounts of contaminating molecules, such as proteins and RNA. The researchers were able to treat the extract with enzymes to degrade proteins (using protease), RNA (using RNase), or DNA (using DNase). Eliminating the proteins or RNA did not alter the transformation of the type R to type S strains. Only the enzymatic degradation of DNA disrupted the transformation, indicating that DNA is the genetic material.
[Nucleic Acid Structure] What is an organic macromolecule composed of nucleotides?
Nucleic acid. The two types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
How was the name nucleic acid coined?
When Swiss physician Friedrich Miescher in 1869 discovered a phosphorous-containing substance from the nuclei in white blood cell in waste surgical bandages, he named the substance nuclein. Later on, they were gound to be acidic molecules, which means they release hydrogen ions (H+) in solution and have a net negative charge at neutral pH. Thus, the name of nucleic acid was coined.
What is an organic molecule having three components: one or more phosphate groups, a five-carbon sugar (either deoxyribose or ribose), and a single or double ring of carbon and nitrogen atoms known as a base?
Nucleotide
What is the structure of of DNA (or RNA) formed by the covalent linkage of nucleotides in a linear manner?
Strand
What are two strands of DNA hydrogen-bonded with each other?
Double Helix. Two DNA strands are twisted together to form a structure that resembles a spiral staircase.
What allows DNA to associate into a compacted structure like a chromosome?
The wide array of different proteins to form chromosomes.
What is the complete genetic material of an organism or species?
The genome
[Review] What are the three components of a nucleotide?
A phosphate group, a 5-carbon sugar, and a nitrogen-containing base.
What pentoses are found in DNA? What about RNA?
Deoxyribose and ribose. This, their phosphate groups, and nitrogen base.
How many different bases are there and how are they categorized?
There are five different bases, only one per any given nucleotide. The bases are categorized into pyrimidines and purines.
What is either bases adenine (A) and guanine (G), which is fused double ring of carbon and nitrogen atoms?
Purines
What is any of the bases thymine (T), cytosine (U), and uracil (U), which have a single ring of carbon and nitrogen atoms?
Pyrimidines
What two bases are only found in DNA or RNA?
Thymine is only found in DNA while Uracil is only found in RNA.
Which pyrimidine(s) is (are) found in both DNA and RNA?
Cytosine
In the 5-carbon sugar molecule, what is denoted as one prime or the first carbon in the numbering scheme? Where is the 5th carbon in these pentoses?
The carbon to the right of the oxygen atom and the scheme rotates clockwise. The 5th carbon is outside of the ring of carbons.
Where are the bases and phosphate groups attached on the 5-carbon sugar molecules in a nucleotide?
Carbon 1 or one prime is attached to the base while five prime or carbon 5 is attached to a phosphate group.
What does deoxy- in deoxyribose denote in this sugar molecule?
It lacks a single oxygen atom covalently bound to the hydrogen atom off of two prime or carbon 2. In relation to ribose, which has a oxygen atom attached to the hydrogen atom off of carbon 2.
What bond in a strand of DNA or RNA links a covalent bond between the phosphate group of one nucleotide and the sugar molecule of the next nucleotide?
Phosphoester bond
Another way to look at this linkage is to notice that a phosphate group connects two sugar molecules, and from this perspective, the linkage in DNA and RNA strands is called a phosphodiester linkage, which has two phosphoester bonds.
What is the linear arrangement of phosphates and sugar molecules in a DNA or RNA strand called?
Backbone. The bases project from the backbone.
How is the backbone of a DNA or RNA strand charged?
Negatively because of the phosphate groups.
What in a DNA or RNA strand, refers to the orientation of the sugar molecules within that strand. Can be 5′ to 3′ or 3′ to 5′?
Directionality. 5’ to 3’ direction when going from top to bottom. 3’ to 5’ direction when going from bottom to top.
What is a key feature of bases based off of their structure?
The sequence.
How is directionality indicate based off of the sequence of bases?
TACG = Thymine-adenine-cytosine-guanine. For directionality, the sequence of strand is abbreviated 5’-TACG-3’
THIS is a critical feature that allows DNA and RNA to store and transmit information. These strands remain the same over time and only change in rare cases of mutation.
What was the important, experimental tool that led to the discovery of DNA double helix?
X-ray diffraction. When a substance is exposed to X-rays, the atoms in the substance cause the X-rays to be scattered.
If the substance has a repeating structure, the pattern of scattering, known as the diffraction pattern, is related to the structural arrangement of the atoms causing the scattering. The diffraction pattern is analyzed using mathematical theory to provide information regarding the three-dimensional structure of the molecule.
What other information was provided from the pattern about DNA in the x-ray diffraction technique? (2)
- Number of nucleotides per turn.
- Consistency of spacing (2-nm) between strands which corresponds to purine (A or G) bonding with a pyrimidine (T or C).
What year did James Watson and Francs Crick propose the structure of DNA and in what journal?
1953 in the journal, Nature. They discovered using ball and stick models that purine bases, A or G, bonds with pyrimidine bases, T or C.
How is the structure of DNA stabilized between base pairs on opposite strands in DNA?
Hydrogen Bonding
What is the structure in which two bases in opposite strands of DNA are held together by hydrogen bonding to each other?
Base pairs
What is the rule that refers to the phenomenon that an A in one DNA strand always hydrogen-bonds with a T in the opposite strand, and a G in one strand always hydrogen-bonds with a C?
AT/GC rule
To follow-on the AT/GC rule, what always bonds with what?
Purines (A and G) always bond with pyrimidines (T and C)
What is the distance for one complete turn of a double helix and roughly how many base pairs does it contain?
3.4 nm in length, 2 nm in width, and comprises of about 10 base pairs.
[Bonus] One nucleotide is .34 nm long hence 3.4 length for 10 base pairs.
What word is used to describe the helix structure in reference to the two strands orientating around each other?
Antiparallel
How many hydrogen bonds exist between adenosine and thymine? What about guanine and cytosine?
2 hydrogen and 3 hydrogen bonds, respectively. The bonds between guanine and cytosine are more stable since they have more bonds.
What is created on the outside of the double-helix structure based off of the asymmetrical spacing and antiparallel orientation of DNA?
A major and minor groove. These play important roles in the binding of proteins that regulate gene transcription.
What is the characteristic of the two strands of DNA that is due to the specific base pairing that occurs between nucleic acids: A pairs only with T (in DNA) or U (in RNA), and G pairs only with C.
This is a complementary characteristic.
What is the arrangement in DNA where one strand runs in the 5´ to 3´ direction and the other strand is oriented in the 3´ to 5´ direction?
Antiparallel
What is a wider groove that spirals around the DNA double helix; provides a location where a protein can bind to a particular sequence of bases and affect the expression of a gene?
Major groove
What is a groove that spirals around the DNA double helix but is smaller than the major groove?
Minor groove
What is the process by which DNA is copied? The original DNA strands are used as templates for the synthesis of new DNA strands.
DNA replication
What do you call the newly made strand in DNA replication?
Daughter strand
What do you call the original strand in DNA replication?
Parental strand
What is the correct model of DNA replication; double-stranded DNA is half conserved following replication, resulting in new double-stranded DNA containing one parental strand and one daughter strand?
Semiconservative mechanism
What is a incorrect model of DNA replication, where both parental strands of DNA remain together (are conserved) following DNA replication. The two newly made daughter strands are also joined together?
Conservative mechanism
What is another incorrect model for DNA replication, segments of parental DNA and newly made DNA are interspersed in both strands following the replication process?
Dispersive mechanism
What did Meselson and Stahl use as a model organism to determine the correct mechanism of action in DNA replication?
Bacterium, Escherichia coli. An important feature of the research involved the use of isotope labeling in Nitrogen.
Using 15N form of nitrogen (heavy) and 14N form of nitrogen (lighter), Meselson and Stahl would let bacteria grow several generations in the heavy medium first. Then, moving the bacteria to a light medium, allowed for the nitrogen source to be of light nitrogen.
Eventually they put the DNA into a gradient that would have the DNA set in a specific place in the gradient. Heaviest would sink to the bottom, heavy and light nitrogenous DNA would be around the middle, and the all light DNA would be around the top.
Using UV light, after the first round of DNA replication, all of the DNA was half-heavy meaning this data was consistent with semiconservative and dispersive mechanisms of DNA replication.
If this experiment was conducted for four rounds of DNA replication (that is, four generations), what would be the expected fractions of light DNA and half-heavy DNA according to the semiconservative model?
The expected fractions would be 1/8 half-heavy and 7/8 light.
What is the DNA strand that is used as a template for RNA synthesis or DNA replication?
Template strand. DNA replication relies on the complementarity of DNA strands according to the AT/GC rule.
What is the region called where nucleotides have access to the template strands after separation in the duplication process?
The replication fork.
After a nucleotide binds to its partner in the replication fork, what is the next bond that is formed?
A covalent bond is formed between the phosphate of one nucleotide and the sugar of the previous nucleotide.
After a nucleotide binds to its partner in the replication fork, what is the next bond that is formed?
A covalent bond is formed between the phosphate of one nucleotide and the sugar of the previous nucleotide.
T/F DNA replication produces two copies of DNA with the same sequence as the original DNA molecule.
True.
DNA replication creates two new double helixes at the same time. Where are these nucleotides attached in reference to the leading and lagging sides of the replication process?
On the leading (left) side of DNA replication, nucleotides occurs towards the direction of the fork. Whereas synthesis for the other newly lagging (right) side, occurs in small segments leading away from the replication fork.
What is the site within a chromosome that serves as a starting point for DNA replication?
Origin of replication
What happens when two DNA strands unwind at the origin of repliction and begin to unwind?
Replication proceeds outward from two replication forks.
What is a name fore this replication outwards from two replication forks at the origin of replication? In other words, The process in which DNA replication proceeds outward from the origin in opposite directions.
Bidirectional replication.
T/F Eukaryotes and bacteria have the same amount of origins of replication.
False. Bacteria DNA genome is rather small so it has one but Eukaryotes have many so replication can happen in a reasonable amount of time.
What completes the replication process in eukaryotes?
When the newly made strands from each origin make contact with each other.
What is a template understanding of what needs to happen in DNA replication? (2)
The strands of the double helix must separate.
The resulting fork must move.
What enzyme uses ATP to separate DNA strands during DNA replication?
DNA helicase
In what direction does DNA helicase move when it is bonded to one of the DNA strands which allows and how does it use ATP?
It travels in the 5’ to ‘3 direction and uses ATP to break hydrogen bonds between base pairs.
The enzyme, DNA helicase, can create knots ahead of the replication fork called supercoils. How are these removed?
By another enzyme called DNA topoisomerase.
How does DNA topoisomerase travel in relation to the replication fork?
Slight ahead of the fork looking for knots.
While the two template DNA strands have been separated, they must remain so until their daughter strands have been made – What is the proteins that binds to both of the single strands of parental DNA and prevents them from re-forming a double helix during DNA replication?
Single-strand binding protein
What is the job of DNA gyrase?
In bacterial cells, it is an essential enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed-circular DNA.
Positive super force coiling is in right handed direction which is the same direction as the double helix in DNA.
Gyrase protein binds to a supercoil molecule and creates a double break through ATP hydrolysis. The break in the strand is repaired and gyrase releases leaving a negative supercoil in bacterial DNA.
When single-strand binding proteins bind to each separated strand of DNA replication, what does it accomplish?
It allows the bases within the template strands to be exposed so they can act as templates for the synthesis of complementary or daughter strands.
What enzyme is responsible for covalently linking nucleotides together during DNA replication?
DNA polymerase
It was discovered in the 1950s and resembles a human hand with the DNA threaded through it.
What strand can DNA polymerase only add nucleotides to when helicase separates the strands?
Only the free 3’ (three prime) end.
In order for DNA polymerase to begin building the daughter strand, a short primer known as RNA primer is synthesized first giving DNA polymerase a starting point.
What are the individual nucleotides with three phosphate groups called which utilize the catalytic site on DNA polymerase to bind to exposed bases via hydrogen bonds in synthesis of a daughter strand?
Deoxynucleoside triphosphates
Referring to the catalytic site on DNA polymerase and the interaction with deoxynucleoside triphosphates, what is accomplished by the active site on the enzyme? (2)
- Bond is broken between the first and second phosphate.
- Attaches resulting nucleotide with one phosphate group (a deoxynucleoside monophosphate) to the 3’ end of a growing strand via a phosphoester bond.
What is significant in the breaking and bonding of the deoxynucleoside via the work of DNA polymerase in regards to net free energy?
This process is exergonic because of the covalent bond breakage which created pyrophosphate. The energy released is used for adjacent nucleotides.
Pyrophosphate is then broken down into two phosphates.
Does the oxygen in a new phosphoester bond come from the sugar or from the phosphate?
The oxygen in a new phosphoester bond comes from the sugar.
[Bonus] What are the rates of DNA polymerase synthesis of DNA in bacteria? What about eukaryotic cells?
500 nucleotides per second in bacteria; 50 nucleotides per second.
What are the other two enzymatic features of DNA polymerase?
- It can elongate a preexisting strand by making DNA.
2. it can synthesize new DNA only in a 5′ to 3′ direction. Antiparallel to the template or parent strand.
Since DNA polymerase cannot begin DNA synthesis on a bare template strand, what is needed to begin its own DNA replication process?
DNA primase. This enzyme is the one that synthesizes a primer for DNA replication.
It is a short segment of RNA, typically 10 to 12 nucleotides in length. This “primes” the DNA replication process.
During DNA replication, what DNA strand made in the same direction that the replication fork is moving? The strand is synthesized as one long continuous molecule.
Leading strand
During DNA replication, what DNA strand made as a series of small Okazaki fragments that are subsequently connected to each other to form a continuous strand?
Okazaki fragments
Short segments of DNA synthesized in the lagging strand during DNA replication.
Lagging strand
What must the leading strand do in order for the lagging strand to add another Okazaki fragment?
At what point is the first and second Okazaki fragments connected?
Elongate which is a property of DNA polymerase.
After the third fragment is added.
Which strand, the leading or lagging strand, is made discontinuously in the direction opposite to the movement of the replication fork?
The lagging strand is made discontinuously in the direction opposite to the movement of the replication fork.
For synthesis of leading and lagging strands in E. coli:
- What are the two different DNA polymerases primarily responsible for DNA replication?
- For the leading strand, DNA primase makes an RNA primer at the origin, and then DNA polymerase III attaches nucleotides in which direction?
- For processivity, a characteristic of DNA polymerase that keeps it from falling off the template stand as it is synthesizing a new daughter strand, is produced by subunit of DNA polymerase III?
- DNA polymerase I and III
- 5’ to 3’ direction and slides towards the replication fork.
- Subunit called a clamp protein.
How does DNA primase keep making primers for the lagging strand?
It jumps back to the fork and lays down another primer. After this occurs, DNA polymerase III synthesizes the remainder of the fragment.
While DNA polymerase III elongates the leading strand, how does DNA polymerase keep synthesizing DNA?
By utilizing each consecutive primer laid down by DNA primase,
What removes the first primer and the consecutive ones after that and replaces it with function DNA bases?
DNA polymerase I
To complete the synthesis of Okazaki fragements within the lagging strand, what must be accomplished (3)? Some of these have been reviewed already.
The RNA primers are removed by DNA polymerase I, which digests the linkages between nucleotides in a 5′ to 3′ direction (away from the fork).
After the RNA primer is removed, DNA polymerase I fills in the vacant region with DNA.
After the DNA has been completely filled in, a covalent bond is missing between the last nucleotide added by DNA polymerase I and the first nucleotide in the adjacent Okazaki fragment. An enzyme known as DNA ligase catalyzes the formation of a covalent bond between these two DNA fragments to complete the replication process in the lagging strand
What enzyme catalyzes the formation of a covalent bond between nucleotides in adjacent DNA fragments to complete the replication process?
DNA ligase
Briefly describe the movement of primase in the lagging strand in this figure. In which direction does it move when it is making a primer, from left to right or right to left? Describe how it must move after it is done making a primer and has to start making the next primer at a new location. Does it have to hop from left to right or from right to left?
When primase is synthesizing a primer in the lagging strand, it moves from left to right in this figure. After it is done making a primer, it needs to hop to the opening of the replication fork to make a new primer. This movement is from right to left in this figure.
[Review] Listing of Proteins in DNA replication
DNA helicase Single-strand binding protein Topoisomerase DNA primase DNA polymerase DNA ligase
Separates double-stranded DNA into single strands
Binds to single-stranded DNA and prevents it from re-forming a double helix
Removes tightened coils ahead of the replication fork
Synthesizes short RNA primers
Synthesizes DNA in the leading and lagging strands, removes RNA primers, and fills in gaps
Covalently attaches adjacent Okazaki fragments in the lagging strand
How does DNA replication make sure very little mistakes (high fidelity) happens?
- First, hydrogen bonding between A and T or between G and C is more stable than hydrogen bonding between mismatched pairs of bases.
- Second, the active site of DNA polymerase is unlikely to catalyze bond formation between adjacent nucleotides if a mismatched base pair is formed.
- Third, DNA polymerase can identify a mismatched nucleotide and remove it from the daughter strand. This event, called proofreading, occurs when DNA polymerase detects a mismatch and then reverses its direction and digests the linkages between nucleotides at the end of a newly made strand in the 3′ to 5′ direction. Once it passes the mismatched base and removes it, DNA polymerase then changes direction again and continues to synthesize DNA in the 5′ to 3′ direction.
What active site on DNA polymerase is responsible for removing errors plus a few more nucleotides?
3’ Exonuclease site
How many different DNA polymerases are produced in E. coli and how many are produced in humans?
5 in E. coli and 12 or more in humans.
What is a region at the ends of eukaryotic chromosomes where a specialized form of DNA replication occurs?
Telomere
How many times is the short nucleotide sequence of a telomere repeated? What is the repeat sequence for humans?
Few dozen to several hundred times.
5’-GGGTTA-3’
Termed a 3’ overhang with no complementary strand.
What enzyme catalyzes the replication of the telomere?
Telomerase which prevents chromosome shortening by attaching many copies of a DNA repeat sequence to the ends of chromosomes.
What does telomerase contain?
Protein and RNA.
Why is telomerase capable of binding to the 3’ overhang region of the telomere?
The RNA part of telomerase is complementary to the DNA repeat sequence.
[Rewind] Why does DNA replication even need telomerase?
Because DNA polymerase is incapable of copying the ends of DNA strands. Without telomerase, DNA replication would shorten DNA strands over time.
Once telomerase binds to the end of the telomere, what happens next in the subsequent steps?
- RNA sequence beyond the binding site functions as a template, allowing telomerase to synthesize a 6-nucleotidesequence at the end of the DNA strand.
- The enzyme then moves to the new end of this DNA strand and attaches another 6 nucleotides to the end. This occurs many times, thereby greatly lengthening the 3′ end of the DNA in the telomere.
What happens after the telomere is lengthened greatly?
This lengthening provides an upstream site for an RNA primer to be made. DNA polymerase then synthesizes the complementary DNA strand. In this way, the progressive shortening of eukaryotic chromosomes is prevented.
What does telomerase use as a template to make the DNA repeat sequence?
Telomerase uses an RNA sequence that it contains as a template to make the DNA repeat sequence.
How is telomerase associated with in cancer?
In 90% of all types of human cancers, telomerase has been found to be present at high levels in the cancer cells. This prevents telomere shortening and may play a role in the continued growth of cancer cells. The mechanism whereby cancer cells are able to increase the function of telomerase is not well understood and is a topic of active research.
[Eukaryotic Chromosomes Start] A typical eukaryotic chromosome may be hundreds of millions of base pairs in length, if they were stretched end to end, how long would they be?
1 meter! Cell nucleus to typically 2-4 um in diameter.
What is a discrete unit of genetic material composed of DNA and associated proteins?
Chromosomes. Eukaryotes have chromosomes in their cell nuclei and in plastids and mitochondria.
How many chromosomes does the human somatic cell have?
46
What is the complex of DNA and proteins that makes up eukaryotic chromosomes?
Chromatin
What is the first way DNA is compacted?
By wrapping itself around a group of proteins called histones.
Histones - A group of proteins involved in the formation of nucleosomes, which aid in the compaction of eukaryotic DNA.
What is the first way DNA is compacted?
By wrapping itself around a group of proteins called histones.
Histones - A group of proteins involved in the formation of nucleosomes, which aid in the compaction of eukaryotic DNA.
What is the structural unit of eukaryotic chromosomes composed of an octamer of histones (eight histone proteins) wrapped with DNA?
Nucleosome. 11 nm in diameter at its largest point.
How many base pairs (bp) of DNA are wrapped around these octamer of histone proteins?
146 - 147 base pairs
How many different types of histone proteins and how many copies of them make up the octamer of histone proteins?
Two molecules each of 4 histone proteins: H2A, H2B, H3, and H4. = 8 total protein molecules.
What relationship exists that allows DNA to be attracted to histone proteins?
The histone proteins are very basic because they contain a large number of positively charged amino acids, namely lysine and arginine.
The negative charges found in the phosphates of DNA are attracted to the positive charges on histone proteins.
What protrudes out of the histone octamer which can be covalently modified and plays a key role in gene regulation?
The amino terminal tail of each histone
What is the region that connects nucleosomes together and how many base pairs does it consist of?
20 to 100 bp, depending on the species and cell type. This region is called the linker region.
What particular histone is bound to the linker region?
H1
Since this structure of histone proteins, wrapped DNA which resembles beads on a string, how much does this structure reduce the length of DNA by?
About 7 times.
What are the nucleosome units organized into a more compact structure?
30-nm fiber (30 nm in diameter)
What causes this nucleosome to shorten another 7 times?
The histone H1 and other proteins are important for this function.
This smaller structure was proposed as a model by Rachel Scherer and Christopher Woodcock in the 1990s.
According to their model, linker regions in the 30-nm structure are variably bent and twisted, with little direct contact between nucleosomes.
[Review] What are the two mechanisms that compact eukaryotic DNA?
The formation of nucleosomes and their arrangement into a 30-nm fiber.
Taken together, these two events folded DNA about 49-fold or times.
What does the third level of compaction of DNA involve? (just the main parts)
- The 30-nm fibers
- A filamentous network of proteins in the nucleus called the nuclear matrix.
What is a filamentous network of proteins that is found inside the nucleus and lines the inner nuclear membrane?
Nuclear matrix. The nuclear matrix serves to organize the chromosomes.
What is a collection of protein fibers that line the inner nuclear membrane; part of the nuclear matrix?
Nuclear lamina (along the edges)
What is a loop of chromatin, often 25,000 to 200,000 base pairs in size, that is anchored to the nuclear matrix?
Radial Loop Domain
What holds the bases of the radial loop domains in place?
Proteins hold the bases of the radial loop domains in place by attaching them to protein fibers or filaments inside the nucleus.
What is the difference between heterochromatin and euchromatin?
Heterochromatin is the highly compacted regions of chromosomes that are usually transcriptionally inactive because of their tight conformation. Euchromatin is the less condensed regions of a chromosome; areas that are capable.
What form of chromatin is the 30-nm fiber that forms radial loop domains?
Euchromatin
What is the difference between heterochromatin loop domains and euchromatin loop domains?
Heterochromatin is much more compacted
What happens to chromosomes when they prepare to divide?
They become even more compacted; each are compacted into heterochromatin. This conformation aids in the metaphase, a stage of eukaryotic cell division.
[Review Start] Why did researchers initially believe that the genetic material was composed of proteins?
Proteins are more biochemically complex than DNA.
Proteins are found only in the nucleus, but DNA is found in many areas of the cell.
Proteins are much larger molecules and can store more information than DNA.
all of the above
both a and c
a
Which component is always different when comparing a nucleotide in a DNA strand to one in an RNA strand?
phosphate group
pentose sugar
nitrogenous base
both b and c
a, b, and c
b
Which of the following equations is accurate concerning DNA base composition?
%A + %T = %G + %C
%A = %G
%A = %G = %T = %C
%A + %G = %T + %C
d
If the sequence of a segment of DNA in one strand is 5′–CGCAACTAC–3′, what is the sequence of the corresponding segment in the opposite strand?
5′–GCGTTGATG–3′
3′–ATACCAGCA–5′
5′–ATACCAGCA–3′
3′–GCGTTGATG–5′
d
Which of the following statements about the process of DNA replication is correct?
New DNA molecules are composed of two completely new strands.
New DNA molecules are composed of one strand from the old molecule and one new strand.
New DNA molecules are composed of strands that are a mixture of sections from the old molecule and sections that are new.
None of the above statements is correct.
b
Meselson and Stahl were able to demonstrate semiconservative replication in E. coli by
using radioactive isotopes of phosphorus to label the original strand and visually determining the relationship of original and new DNA strands.
using different enzymes to eliminate old strands from DNA.
using isotopes of nitrogen to label the DNA and determining the relationship of original and new DNA strands by density differences of the new DNA molecules.
labeling viral DNA before it was incorporated into a bacterial cell and visually determining the location of the DNA after centrifugation.
c
During replication of a DNA molecule, the daughter strands are not produced in exactly the same manner. One strand, the leading strand, is made toward the replication fork, while the lagging strand is made in fragments in the opposite direction. This difference in the synthesis of the two strands is the result of which of the following?
DNA polymerase is not fast enough to make two leading strands of DNA.
The two template strands are antiparallel, and DNA polymerase makes DNA only in the 5′ to 3′ direction.
The lagging strand is the result of DNA breakage due to UV light.
The cell does not contain enough nucleotides to make two complete strands.
b
In living cells, chromosomes consist of
DNA and RNA.
DNA only.
RNA and proteins.
DNA and proteins.
RNA only.
d
A nucleosome is
a dark-staining body composed of RNA and proteins found in the nucleus.
a protein that helps organize the structure of chromosomes.
another word for a chromosome.
a structure composed of DNA wrapped around eight histones.
the short arm of a chromosome.
d
The conversion of euchromatin into heterochromatin involves
the formation of more nucleosomes.
the formation of less nucleosomes.
a greater compaction of loop domains.
a lesser compaction of loop domains.
both a and c.
c
What are the four key criteria that the genetic material must fulfill? What was Griffith’s contribution to the study of DNA, and why was it so important?
The genetic material must contain the information necessary to construct an entire organism. The genetic material must be accurately copied and transmitted from parent to offspring and from cell to cell during cell division in multicellular organisms. The genetic material must contain differences that can account for the known variation within each species and among different species. Griffith discovered something called the transformation principle, and his experiments showed the existence of biochemical genetic information. In addition, he showed that this genetic information can move from one individual to another of the same species. In his experiments, Griffith took heat-killed type S bacteria and mixed them with living type R bacteria and injected them into a live mouse, which died after the injection. By themselves, these two strains would not kill the mouse, but when they were put together, the genetic information from the heat-killed type S bacteria was transferred into the living type R bacteria, thus transforming the type R bacteria into type S.
A double-stranded DNA molecule contains 560 nucleotides. How many complete turns occur in this double helix?
Since DNA is double stranded, 560 nucleotides form 280 bp. With 10 bp per turn, this DNA double helix will have 28 complete turns.
Discuss how the structure of DNA underlies different aspects of its function.
In a DNA double helix, the two strands hydrogen-bond with each other according to the AT/GC rule. This provides the basis for DNA replication. In addition, as described in later chapters, hydrogen bonding between complementary bases is the basis for the transcription of RNA, which is needed for gene expression. The sequence of bases within DNA strands have the function of storing information such as the sequence of amino acids within a polypeptide.
A trait that some bacterial strains exhibit is resistance to being killed by antibiotics. For example, certain strains of bacteria are resistant to the drug tetracycline, whereas other strains are sensitive to this antibiotic. Describe an experiment you would carry out to demonstrate that tetracycline resistance is an inherited trait carried in the DNA of the resistant strain.
[Your own response]
How might you provide evidence that DNA is the genetic material in mice?
[Your own response]
A child has a disease that is causing severe growth delays and rapid aging. His cells are assayed, and it is noticed that there is a severe decrease in DNA synthesis compared to normal cells. When DNA from his cells is examined many, small, single-stranded fragments of about 1000 base pairs were found. Which enzyme/protein is likely to be defective in this child?
Question 1 options:
helicase
DNA polymerase
DNA ligase
Primase
b?
A researcher has discovered a mouse that has two forms of DNA polymerase. One form adds bases to the 3’ end and one adds bases to the 5’ end. What does this mean for the mouse?
Question 2 options:
It will not make Okazaki fragments
It will not be able to make a complementary daughter strand
Its DNA will not be unwound for replication
Its DNA will not be compacted around histones
b WRONG
If DNA polymerase is not functioning normally, what is likely to occur?
Question 3 options:
The DNA will not be unwound for replication
Complementary bases will not be added to create a daughter strand
Okazaki fragments will not be sealed together
DNA will not be compacted around histones
b
A researcher has discovered a mouse that lacks the correct form of the enzyme primase. What does this mean for the mouse?
Question 4 options:
It will not make Okazaki fragments
It will not be able to make a complementary daughter strand
Its DNA will not be unwound for replication
Its DNA will not be compacted around histones
b
Who discovered that DNA was actually the genetic material or transforming factor that could convert nonvirulent R-type Streptococcus pneumonia bacterium to the virulent S-type?
Question 5 options:
Weismann and Nageli
Griffith
Avery, MacLeod, and McCarty
Hershey and Chase
Watson, Crick, Wilkins, and Franklin
b WRONG
During DNA replication, new bases are always added to the 3’end. This means that one side will have a leading strand and the other side
Question 6 options:
Will not replicate its DNA
Will not require an RNA primer
Will have a lagging strand made of Okazaki fragments
Will not require DNA polymerase
c
One of the characteristics of our genetic material was that it needed to have variation. The variation in our DNA comes from
Question 7 options:
The shape of the DNA
The sequence of bases in the DNA
The tertiary sequence of the DNA
The two dimensional shape of the DNA
b
Griffiths (1928) mixed heat-killed ‘S’ bacteria with ‘R’ bacteria and injected a mouse with both types of bacteria. As a result, the mouse died and Griffiths obtained living ‘S’ bacteria from the dead mouse. How can you explain this phenomenon?
Question 8 options:
The DNA from the ‘S’ bacteria with the gene responsible for capsule formation was transferred to the ‘R’ bacteria when the strains were mixed. This gene transformed the ‘R’ bacteria into ‘S’ bacteria, allowing it to produce a capsule and evade the mouse’s immune system.
The protein from the ‘S’ bacteria responsible for DNA replication was transferred to the ‘R’ bacteria when the strains were mixed. This protein transformed the ‘R’ bacteria into ‘S’ bacteria, allowing it to reproduce at an extremely high rate and overwhelm the mouse’s immune system.
The living ‘R’ bacteria were able to regenerate the heat-killed ‘S’ bacterial cells. The regenerated ‘S’ bacteria were highly virulent and killed the mouse.
The protein from the ‘S’ bacteria responsible for capsule formation was transferred to the ‘R’ bacteria when the strains were mixed. This protein transformed the ‘R’ bacteria into ‘S’ bacteria, allowing it to produce a capsule and evade the mouse’s immune system.
a
Based on the information provided on this chart, you can conclude
Locus Mother Child Male A Male B CSFPO 10,11 10,13 9,13 8,13 TPOX 5,5 5,11 7,11 9,11 D7S820 12,15 12,12 4,12 4,15 D13S27 8,10 11,11 9,11 8,11 Question 9 options:
The child has a genetic mutation at the CSFPO locus
Male A is the brother of the child
Male A and Male B are identical twins
The child is homozygous at the D13S27 locus
b WRONG
Beginning with the simplest level of structure, which order of organization of genetic material is CORRECT?
Question 10 options:
DNA, nucleotide, gene, genome, chromosome.
nucleotide, DNA, gene, chromosome, genome.
DNA, nucleotide, gene, chromosome, genome.
nucleotide, DNA, gene, genome, chromosome.
nucleotide, DNA, chromosome, gene, genome.
b
Which of these is an advantage of semiconservative replication?
Question 11 options:
It is faster
It is less prone to error
It requires less energy
It requires fewer enzymes
b
Okazaki fragments are needed because
Question 12 options:
DNA replication only occurs at the ribosomes
Transcription only occurs in the nucleus
A only binds to T during translation
DNA replication only occurs in one direction
d
After replication you have two molecules of DNA. What is true about these molecules
Question 13 options:
Each is made of one parent strand and one daughter strand
One is made of two parent strands and the other is made of two daughter strands
Each is made of one parent strand
Each is made of one daughter strand
a
Which is of these is the complementary DNA strand to the following template DNA strand? 5’-ATTCGGTAACCC-3’
Question 14 options:
5’- TAAGCCATTGGG - 3’
3’- TAAGCCATTGGG - 5’
5’- UAAGCCUAACCC - 3’
3’ -UAAGCCUAACC - 5’
b
Which is of these is the complementary DNA strand to the following template DNA strand? 5’-ATTCGGTAACCC-3’
Question 14 options:
5’- TAAGCCATTGGG - 3’
3’- TAAGCCATTGGG - 5’
5’- UAAGCCUAACCC - 3’
3’ -UAAGCCUAACC - 5’
b
You are trying to determine parentage of a specific child and have done microsatellite analysis. At a locus named LPOG you find that the mom’s genotype is 12, 4 and the child’s is 12, 8. What does this tell you?
Question 15 options:
The child must be adopted, as the woman you tested cannot be the mother
The father’s genotype at that locus must have 8 repeats
The father’s genotype at that locus must have 12 repeats
None of the above
b
Which molecule carries the genetic instructions for the physical characteristics of living organisms?
Multiple choice question.
Lipids
Proteins
DNA
Carbohydrates
DNA
In order for the genetic material to fulfill its role in cells, it must meet which of the following criteria?
Multiple select question.
Diversity
Replication
Variation
Information
Continuity
Transmission
Replication
Variation
Information
Transmission
What is the composition of a chromosome?
Multiple select question.
Lipids
DNA
RNA
Polysaccharides
Protein
DNA
Protein
The English microbiologist Frederick Griffith discovered transformation while experimenting with a bacterium now classified as ______.
Multiple choice question.
Streptococcus pneumoniae
Mycoplasma pneumoniae
Staphylococcus aureus
Streptococcus pyogenes
Streptococcus pneumoniae
The two nucleic acids are
Blank 1: DNA, deoxyribonucleic acid, deoxyribonucleic, or ADN
Blank 2: RNA, ribonucleic acid, ribonucleic, or ARN
DNA controls the ______.
Multiple select question.
environment of organisms
ability of a fertilized egg to develop into an adult organism
characteristics of organisms
ability of a fertilized egg to develop into an adult organism
characteristics of organisms
Nucleotides contain a sugar, a phosphate, and a(n) __________
base.
nitrogen
True or false: Only three criteria are needed for the genetic material to fulfill its role. These are information, variation, and replication.
False
The presence of a sugar called ___________
would definitively identify a nucleic acid as RNA.
ribose
The cell structure that contains DNA is the ______.
Multiple choice question.
cytosol
chromosome
nucleolus
ribosome
chromosome
The bacterium Streptococcus pneumoniae causes the disease __________
, which can be fatal.
pneumonia
Which of the following is found in DNA and not in RNA?
Multiple choice question.
Cytosine
Thymine
Adenine
Uracil
Guanine
Thymine
Adjacent nucleotides in the same DNA strand are held together by covalent bonds known as ____________
bonds.
Phosphodiester
Which of the following is found in DNA but not in RNA?
Multiple choice question.
Ribose
Pentose sugar
Pyrimidines
Purines
Deoxyribose
Deoxyribose
In a DNA double helix, the phosphate groups and sugars ______.
Multiple choice question.
project from the backbones toward the inside of the helix
project from the backbones toward the outside of the helix
form the backbones
form hydrogen bonds with each other
form the backbones
What is the composition of a chromosome?
Protein
DNA
Directionality refers to the orientation of ______.
Multiple choice question.
sugar molecules in a DNA strand
the axis of the double helix
purines to pyrimidines
sugar molecules in a DNA strand
The critical feature that allows for the storage and transmission of information is the ___________
of bases in DNA and RNA.
Blank 1: sequence, order, or arrangement
The presence of the nitrogenous base
___________
would indicate that a nucleic acid is RNA, not DNA.
Uracil
X-ray diffraction was used to suggest that there was a ______ amount of space between the two backbones of a DNA double helix where a purine bonds with a pyrimidine.
Multiple choice question.
2 nm
1 nm
6 nm
10 nm
2 nm
Who determined the double helix structure of DNA using ball-and-stick models and experimental observations by Wilkins and Franklin?
Multiple choice question.
Avery, MacLeod, and McCarthy
Watson and Crick
Hershey and Chase
Meselson and Stahl
Watson and Crick
Select all that apply
How many hydrogen bonds are formed between adenine and thymine in the double DNA helix?
Multiple select question.
1
one
2
3
two
three
2
two
The orientation of sugar molecules within a DNA strand is referred to as __________
. For example, a strand is said to be 5’ to 3’ or 3’ to 5’.
directionality
The sequence of bases in DNA and RNA allows for which of the following?
Multiple select question.
Storage of energy
Strengthening of the cell
Storage of information
Transmission of information
Storage of information
Transmission of information
X-ray ________________
patterns are mathematically related to the structural arrangement of atoms causing a scattering pattern, which can be used to explain the three dimensional structure of molecules.
Diffraction
The double-helix structure of DNA was proposed by \_\_\_\_\_\_\_\_\_\_\_ and \_\_\_\_\_\_\_\_\_\_\_\_\_ . (Please include FAMILY names only)
Blank 1: Watson or James Watson
Blank 2: Crick or Francis Crick
Which bases are connected by two hydrogen bonds?
Multiple choice question.
Thymine and cytosine
Adenine and thymine
Cytosine and guanine
Guanine and adenine
Adenine and thymine
The critical feature that allows for the storage and transmission of information is the ________________
of bases in DNA and RNA.
sequence, order, or arrangement
Guanine forms
_______ hydrogen bonds with cytosine.
3
Who determined the double helix structure of DNA using ball-and-stick models and experimental observations by Wilkins and Franklin?
Multiple choice question.
Meselson and Stahl
Watson and Crick
Avery, MacLeod, and McCarthy
Hershey and Chase
Watson and Crick
Of the following choices, which are base paired properly?
Multiple select question.
A-T
A-G
C-G
T-G
C-T
A-T
C-G
The orientation of sugar molecules within a DNA strand is referred to as __________. For example, a strand is said to be 5’ to 3’ or 3’ to 5’.
Directionality
Cytosine and guanine form this many hydrogen bonds.
3
DNA template strands are referred to as ______ strands, while the newly synthesized strands are referred to as ______ strands.
Multiple choice question.
lagging; leading
parental; daughter
daughter; parental
leading; lagging
parental; daughter
In DNA, adenine normally pairs with ____________
and cytosine normally pairs with _____________
.
thymine; guanine
During DNA replication, how many strands of DNA are used as templates to synthesize new strands?
1
0
2
2
An origin of replication is a sequence in a chromosome that ______.
Multiple choice question.
initiates RNA synthesis
initiates protein synthesis
initiates DNA synthesis
facilitates chromosome separation during cell division
initiates DNA synthesis
DNA replication is described as ______ because DNA replication proceeds outward from two replication forks.
Multiple choice question.
bidirectional
unidirectional
antiparallel
hybrid
bidirectional
All models of DNA replication include ______.
Multiple select question.
daughter strands
random strands
parental strands
hybrid strands
daughter strands
parental strands
The Meselson and Stahl experiments supported this method of replication.
Multiple choice question.
Semiconservative
Dispersive
Conservative
Semiconservative
Why do eukaryotic cells have multiple origins of replication?
Multiple choice question.
So that both strands of DNA can serve as templates to produce new strands
So that the new strands can meet at the ends of the circular chromosomes
To ensure timely replication of multiple, relatively large chromosomes
To ensure timely replication of multiple, relatively large chromosomes
During DNA replication, new strands are synthesized from __________
strands on the original molecule.
template
What DNA enzyme covalently links nucleotides together?
Multiple choice question.
Phosphatase
Topoisomerase
Polymerase
Helicase
Polymerase
he site within a chromosome where DNA replication begins is termed the _________
of replication.
origin
The enzyme DNA polymerase attaches a nucleotide to the ______ end of a growing strand via a ______ bond.
Multiple choice question.
5’ ; hydrogen
3’ ; hydrogen
3’ ; phosphoester
5’ ; phosphoester
3’ ; phosphoester
This term refers to DNA replication proceeding outward from two replication forks.
Multiple choice question.
Parallel
Bidirectional
Antiparallel
Bidirectional
Leading strands are synthesized ?
Lagging strands are synthesized ?
Leading strand
matches
Choice, Synthesized continuouslySynthesized continuously
Lagging strand
matches
Choice, Synthesized in small fragments that are later connectedSynthesized in small fragments that are later connected
During the replication of DNA, the lagging strand is synthesized as a series of small fragments called __________
fragments.
Okazaki
Which types of cells have more than one origin of replication?
Multiple choice question.
Eukaryotes
Prokaryotes and eukaryotes
Prokaryotes
Eukaryotes
DNA polymerase can detect a mismatched nucleotide and remove it from the daughter strand. It does so by digesting the linkages in the 3’ to 5’ direction to remove the incorrect base and then changing direction to synthesize again in the 5’ to 3’ direction. This process is called
.
proofreading
During DNA replication, the enzyme that covalently links nucleotides to synthesize new DNA strands is DNA __________
polymerase
A telomere
Multiple choice question.
is double stranded
has a 5’ overhang
has a 3’ overhang
has a 3’ overhang
This enzyme works by breaking a bond between the first and second phosphate and attaching a nucleotide dNMP to the 3’ end of the DNA strand via a phosphodiester bond.
Multiple choice question.
Topoisomerase
Helicase
Primase
Polymerase
Polymerase
DNA is compacted by wrapping itself around a group of proteins called
Multiple choice question.
histones
chromosomes
nucleosomes
histones
What can explain the remarkably high fidelity for DNA replication?
Multiple select question.
The hydrogen bonding between AT and CG pairs is more stable than between mismatched pairs.
DNA polymerases that are prone to make errors are destroyed by the cell prior to replication.
DNA polymerase can identify and replace mismatched nucleotides.
DNA polymerase is unlikely to catalyze bond formation between adjacent nucleotides if a mismatched base pair is formed.
The hydrogen bonding between AT and CG pairs is more stable than between mismatched pairs.
DNA polymerase can identify and replace mismatched nucleotides.
DNA polymerase is unlikely to catalyze bond formation between adjacent nucleotides if a mismatched base pair is formed.
This is a region at the ends of eukaryotic chromosomes.
Multiple choice question.
Histone
Chromatin
Telomere
Nucleosome
Telomere
A nucleosome is a repeating structural unit of eukaryotic ______.
Multiple choice question.
RNA
polymerases
chromatin
ribosomes
chromatin
An octamer of histone proteins contains two of each of the following
H3
H4
H2B
H2A
The 30-nm fiber is comprised of _______________
units organized into a more compact structure.
nucleosome
The repeating structural unit of eukaryotic chromatin is the _________
nucleosome
This enzyme works by breaking a bond between the first and second phosphate and attaching a nucleotide dNMP to the 3’ end of the DNA strand via a phosphodiester bond.
Multiple choice question.
Topoisomerase
Polymerase
Primase
Helicase
Polymerase
