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IB HL Biology > 7.1 DNA structure and replication > Flashcards

7.1 DNA structure and replication Flashcards

1
Q

What proteins is eukaryotic DNA vs. prokaryotic DNA associated with?

A

-Eukaryotic DNA is always associated with basic (alkaline) and positively charged proteins called histones.

-This is in contrast to prokaryotic DNA, which lacks histones, and is therefore often referred to as ‘naked’ DNA.

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2
Q

Describe the structure of a nucleosome

A

-A nucleosome consists of a length of DNA of about 150 base pairs, wrapped around a core of eight histones (which are actually four pairs of four different histones) and a special histone named H1.

-DNA is acidic and negatively charged, so the bonding with the histones neutralises the DNA.

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3
Q

Diagram of a nucleosome

A
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4
Q

Why are nucleosomes linked and what is this called?

A

-The nucleosomes are linked because the DNA strand from one nucleosome flows directly into the next nucleosome.

-This section of DNA is called a DNA linker.

-The overall appearance of DNA in this form has been called a string of ‘beads’.

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5
Q

Diagram showing the nucleosomes, the DNA fibre and a chromosome

A
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6
Q

Why is a certain amount of packaging (folding, coiling, and re-coiling) required to fit the genetic material into the nucleus?

A

Because some eukaryotes have large genomes.

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7
Q

How is packaging done to fit the genetic material into a eukaryotic nucleus?

A

-Nucleosomes help to supercoil the DNA while still ensuring appropriate access to it.

-Access to DNA occurs when the coils unwind and histones are moved out of the way so that DNA can be copied or transcribed.

-Nucleosomes can be considered to be the repeat units of eukaryotic chromatin, which is further coiled to form chromosomes.

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8
Q

What does a eukaryotic chromosome consist of?

A

A single linear molecule of double-stranded DNA plus proteins.

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9
Q

What is structure X in the diagram of a nucleosome?

A

Histone

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10
Q

What is the function of the nucleosome?

A

To supercoil DNA

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11
Q

What type of cells have DNA associated with histones?

A

Eukaryotic

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12
Q

What does DNA replication rely on?

A

Base pairing

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13
Q

Give an overview of how Watson and Crick eventually worked out base pairing (reword?)

A

-It took Watson and Crick a long time to work out base pairing.

-They were trying to assemble a compact molecule of DNA because the X-ray diffraction work of Franklin suggested this type of model.

-The DNA molecule also needed to be stable because of its function as genetic material.

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14
Q

What properties does base-pairing allow the double helix to have?

A

-The hydrogen bonding between the purine and the pyrimidines.

-Two hydrogen bonds occur between adenine (A) and thymine (T), and three hydrogen bonds occur between guanine (G) and cytosine (C).

-The slightly positive charge on T and a slightly negative charge on A allow the two bases to bond together during complementary base pairing.

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15
Q

How was a mechanism for DNA replication presented? (reword?)

A

-Once it became clear that DNA forms a double helix with antiparallel strands bonded together by complementary base pairing, a mechanism for DNA replication also presented itself.

-If the double helix of a single DNA molecule was separated, each strand could be used to create the matching new strand through complementary base pairing, resulting in two new identical molecules.

-If, on one strand, the bases T and C occurred successively, automatically on the opposite strand A and G would be present, because A can only pair with T and C can only pair with G.

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16
Q

Diagram of double-stranded DNA showing antiparallel strands and base pairing

A
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17
Q

What are purines and pyrimidines and how do they bond in base pairing?

A

-Purines are: Guanine and Adenine (they contain two rings in their structure).

-Pyrimidines are: Thymine and Cytosine (they contain one ring in their structure).

-In DNA base pairing, a pyrimidine is always bonded to purine.

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18
Q

How does DNA replication progress?

A

-In a semi-conservative way.

-However, the details of DNA replication differ between eukaryotes and prokaryotes.

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19
Q

How does DNA replication differ between eukaryotes and prokaryotes?

A

-The main difference is that in eukaryotes, replication can be initiated at various points along the DNA molecule, while it can be started at only one position on prokaryotic DNA.

-This ensures more efficient DNA replication in eukaryotes.

-You are expected to study the prokaryotic system only.

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20
Q

Diagram showing DNA replication in prokaryotes versus DNA replication in eukaryotes

A
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21
Q

Describe the role of enzymes in DNA replication

A

-DNA replication is carried out by a complex system of enzymes.

-The most important ones are helicase, DNA gyrase, DNA primase, DNA ligase, as well as DNA polymerase I and III.

-The role played by each one of these enzymes in DNA replication should be known.

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22
Q

More info needed on rates of replication and size of human genome?

A

-The rate of replication is approximately 100 nucleotides per second in eukaryotes while it can be as high as 1000 nucleotides per second for prokaryotes.

-The human genome has around 3 billion base pairs per haploid set of chromosomes, so 6 billion base pairs have to be replicated during the S phase of the cell cycle.

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23
Q

How does efficiency change when a DNA molecule is replicated?

A

When a DNA molecule is replicated, efficiency is improved if it progresses in two directions.

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24
Q

DNA replication requires two ___

A

Replication forks

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25
Diagram of semi-conservative DNA replication
26
How do helicase, SSBPs, and gyrase work together?
-First of all, helicase binds to the origin of replication and breaks hydrogen bonds between base pairs to unwind the DNA double helix. -Single-strand binding proteins then bind to the single strands formed to keep them apart to allow time for the DNA sequence to be copied. -The two separated strands act as templates for the replication process. -As helicase moves along the DNA molecule, it causes supercoiling and tension on the region ahead. -This is relieved by the enzyme DNA gyrase, which moves in advance of helicase.
27
What happens to free nucleoside triphosphates when they bind to their template (during DNA replication)?
They lose their two extra phosphate groups to generate energy, which is used to add the nucleotide to the growing polynucleotide chain.
28
What is the leading strand?
The strand of DNA that is being replicated continuously in the 5' to 3' direction by continuous polymerisation at the 3' growing tip.
29
What is the lagging strang?
The strand of DNA that is replicated discontinuously in small fragments in the 5' to 3' direction away from the replication fork.
30
What happens on the leading strand during DNA replication?
-DNA polymerase III, the enzyme that adds DNA nucleotides to the strands, can only add a nucleotide to the 3' OH group of the deoxyribose. -So, on the leading strand, the DNA polymerase follows the helicase, separating the strands and adding the DNA nucleotides. -Because no DNA polymerase enzyme can initiate a new DNA on its own, an RNA primer is needed once for this leading strand
31
What happens on the lagging strand during DNA replication?
-Because no DNA polymerase enzyme can initiate a new DNA on its own, an RNA primer is needed once for this leading strand. -However, this is not possible on the lagging strand, because the last nucleotide ends with a 5' phosphate group. -So, on the lagging strand, a DNA primase first makes short RNA primers (these primers are later removed by DNA polymerase I and substituted with a short DNA segment), which allow the DNA polymerase III to add DNA nucleotides to the 3' OH of the RNA primer. -Many such primers are made as a scaffold for the DNA polymerase III. -It synthesizes short DNA fragments called Okazaki fragments. -The result is two new strands, both based on the template of the old DNA molecule.
32
What are Okazaki fragments?
Short DNA fragments, which are joined together by DNA ligase to form a complete DNA strand.
33
Why does the leading strand require one primer?
Since DNA polymerase III needs a 3' OH group to start the polymerisation process, even the leading strand requires one primer.
34
What are RNA primers?
Short RNA chains of about 10 bases used as a starting point for DNA replication by DNA polymerase III. They are synthesised by DNA primases.
35
In what direction does DNA replication progress and why?
DNA replication always progresses from 5' to 3', because DNA polymerase III ( three ) can only add nucleotides to the 3' OH group of the deoxyribose.
36
Cytosine makes up 42% of the nucleotides in a sample of DNA from an organism. Approximately what percentage of the nucleotides in this sample will be thymine?
8% If there is 42% of C then there must be 42% of G as well since G pairs with C. That leaves 16% for A and T together. So, T is 16÷2=8%.
37
What is meant by the description 'antiparallel' regarding the strands that make up DNA?
The 5' to 3' direction of one strand runs counter to the 3' to 5' direction of the other strand.
38
What components does an Okazaki fragment have?
RNA primer, DNA fragment
39
A biochemist isolated and purified molecules needed for DNA replication. When she added some DNA, replication occurred but the DNA molecules were defective. Each consisted of a normal DNA strand paired with numerous segments of DNA a few hundred nucleotides long. What had she probably left out of the mixture?
-DNA ligase -The scientist had DNA molecules that consisted of unlinked Okazaki fragments in one half of the molecule. -DNA ligase is necessary to join the Okazaki fragments together on the lagging strand.
40
What is the reason that the leading and lagging strands of DNA are synthesised differently?
DNA polymerase III can only join new nucleotides to the 3' end of the growing strand.
41
Which enzyme unwinds the DNA double helix during replication?
Helicase
42
Explain how every base in a DNA molecule is part of a gene
Non-coding sequences are found everywhere in eukaryotic genomes, and some genomes have more than others.
43
How much of the human genome does non-coding DNA account for?
More than 98%
44
What is non-coding DNA?
-DNA sequences within a genome that do not consist of the information to make a protein. -In other words, these DNA bases are never represented within the amino acid sequence of expressed proteins. -This does not mean that non-coding DNA does not have a function. -DNA is 'expensive' to maintain, so, from an evolutionary viewpoint, it should have a function, but we do not always know what that function is.
45
What elements do the regions of DNA that do not code for proteins include?
-Regulators of gene expression -Introns -Telomeres -Genes for tRNAs
46
What is the function of regulators of gene expression?
-These are DNA sequences that regulate gene expression in various ways. -For instance, promoters are sequences that occur just before genes and act as a binding point for the RNA polymerase enzymes that catalyse the transcription process. -Other DNA sequences may act as binding sites for proteins that either increase or decrease the rate of transcription; these are known as enhancers and silencers, respectively.
47
What is the function of introns?
-These are DNA base sequences found within eukaryotic genes that get removed at the end of transcription. -They do not contribute to the amino acid sequence of the polypeptide made from the gene.
48
What is the function of telomeres?
-These are repetitive sequences that protect the ends of the chromosome. -Telomeres help ensure that DNA is replicated correctly. -With every cell division, short stretches of DNA are lost from the telomeres.
49
What is the function of genes for tRNAs?
These genes code for RNA molecules that do not get translated into proteins, but instead fold to form tRNA molecules that play an important role in translation.
50
Image of telomeres located at each end of the chromosome (false color image of a chromosome)
51
What is a tandem repeat?
A sequence of two or more DNA base pairs that is repeated in such a way that the repeats lie end-to-end on the chromosome.
52
What do tandem repeats generally form part of?
Non-coding DNA, though they may be present in protein-coding regions.
53
How can tandem repeats be used for identification in DNA fingerprinting?
A tandem repeat located at a single genetic locus, in which the number of repeated DNA segments varies from individual to individual, is frequently used for identification in DNA fingerprinting.
54
Diagram of the variation of tandem repeats in three different individuals
55
How can tandem repeats be used in DNA profiling, testing, or typing?
-DNA profiling, also called DNA fingerprinting, DNA testing or DNA typing is a technique used to identify individuals by analysing their DNA. -Because tandem repeats vary among individuals, differences in these regions can be analysed to produce a DNA profile. -Human DNA profiles have various uses including the identification of the origin of a DNA sample from a crime scene, tests for parentage and in genealogical research.
56
What are the steps of DNA profiling?
1) Collection of samples and extraction of DNA 2) Amplification (copying) of the DNA region containing tandem repeats by PCR 3) Separation of the DNA fragments using gel electrophoresis.
57
Diagram showing DNA profiling of two individuals and how they differ in the number of tandem repeats and how that is visualised (shown) on a gel (reword?)
58
Describe the tandem repeats for each individual in this diagram of a DNA profile
-In Individual #1, you can see that for allele A6 there are five repeats of the GC tandem (10 base pairs), but for allele A2, there are only two repeats, so that allele is shorter (4 base pairs). -When these two alleles are separated by electrophoresis, the larger A6 segment is separated from the smaller A2 segment. -These differences can be clearly seen on the gel. -The pattern on the gel of each individual’s alleles at each locus forms the DNA fingerprint.
59
The DNA profiles that follow represent four different individuals. Who is the child of whom?
-C is the child of A and B. -All the DNA fragments for C can be traced to either A or B.
60
When DNA profiling is used to analyse the DNA of individuals, which parts of the DNA are used?
Short tandem repeats
61
What is DNA sequencing?
-This is the method used for deducing the precise order of nucleotides within a DNA molecule. -Since all DNA molecules have the same sugar phosphate backbone, the main role of DNA sequencing is to determine the order of the four bases (adenine, guanine, cytosine and thymine) in a DNA strand.
62
What different purposes is DNA sequencing used for?
-DNA sequencing is used for many purposes: DNA profiling, paternity suits, forensics, cancer analysis and genome studies. -Frederick Sanger published the principles of DNA sequencing in 1977.
63
What is Sanger's technique called and what is it based on?
-His technique is called the Dideoxy Chain Termination Method. It is based on the fact that DNA polymerase needs a 3' OH group of the preceding nucleotide to add another nucleotide to the DNA strand. -If a dideoxy nucleotide (a 'normal' DNA nucleotide but lacking the oxygen atom at the 3' OH group) is added to the mixture, and this nucleotide is built into the growing DNA strand, no further nucleotides can be added and the reaction stops.
64
Diagram of two different nucleotides- deoxyadeosine and dideoxyadenosine
65
What method do modern DNA sequencers use?
-They make use of the Dideoxy Chain Termination Method and add a fluorescent dye to the four dideoxynucleotides so that the base present when replication stops can be recognised. -From this, the base on the parent strand is deduced.
66
Diagram showing the basics of the dideoxy chain terminating sequencing method
67
What does dNTP stand for?
Deoxyribose nucleotide triphosphate
68
What does ddNTP stand for?
Dideoxyribose nucleotide triphosphate
69
Why is each nucleotide at every position in the original sequence (in DNA sequencing) known from analyzing these fragments?
-Because so many fragments of DNA are created with each of the four different types of ddNTPs (A, C, T, and G), there is a DNA fragment of every possible length, and it is known which of the nucleotides is at the end of each of these fragments. -So, each nucleotide at every position in the original sequence is known from analysing these fragments.
70
Why might a laboratory be using dideoxynucleotides?
To sequence a DNA fragment
71
What is base sequencing?
A process that allows the precise order of bases in a DNA strand to be determined.
72
What is the purpose of base sequencing?
To determine the order of nitrogen bases in a sample of DNA.
73
What is the relationship between Rosalind Franklin and Maurice Wilkins?
-Franklin was working as a research associate in Wilkins' lab in the 1950s at King's College, London. -Though both of them were working on X-ray diffraction of DNA, it was Rosalind's work that proved useful in unravelling the DNA structure.
74
What technology did Rosalind Franklin develop?
-Franklin developed a better camera for the X-ray diffraction detectors, which enabled her to analyse the DNA crystals. -X-ray diffraction is based on the principle that X-rays are scattered when they pass through different material. -The scattering is called diffraction, and patterns in diffraction indicate properties of the crystals.
75
Explain how X-rays are scattered (diffracted) in X-ray diffraction
-Since X-rays affect photographic film in the same way as visible light (turning it black), the scattering pattern can be visualised on a radiogram. -Biological material, such as DNA, can be used in this technique.
76
Image of X-ray diffraction of DNA It is from a DNA sample that came from Watson and Crick's labs in Cambridge University, UK. The radiogram shows the distance between the base pairs, as well as the turns of the helix (3.4 nm). Franklin was able to measure other features of the DNA molecule, including the distance between the repeats.
77
What was Franklin able to measure from X-ray diffraction of DNA?
She was able to measure other features of the DNA molecule, including the distance between the repeats.
78
How was Rosalind Franklin's data a crucial element in the discovery of the structure of DNA?
The X-ray data obtained by Franklin was shown to Watson and Crick by Maurice Wilkins, allowing them to confirm their ideas on the three-dimensional structure for DNA.
79
Who carried out X-ray diffraction experiments leading to the determination that DNA was a helical molecule?
Rosalind Franklin
80
What type of observation was made from Rosalind Franklin's X-ray diffraction data?
Structural details of DNA's physical shape
81
What controversy was there about what genetic material was there before the Hershey-Chase experiment?
-For a long time, scientists deliberated whether genetic material was protein or DNA. -Most biologists were aware of the role that chromosomes play in heredity, but chromosomes consist of DNA and protein.
82
What did Alfred Hershey and Martha Chase's experiment show?
They convinced the scientific community that it was DNA, and not protein, that made up genetic material.
83
Give an overview of the Hershey-Chase experiment
-They used a T2 bacteriophage, which is a virus that infects bacterial cells. -This virus injects its DNA into the bacterial cell while its protein coat stays on the outside.
84
Image of bacteriophages (virus) injecting DNA into a bacterial cell
85
Describe Hershey and Chase's method
-Hershey and Chase used radioactive phosphorus and sulfur to label the DNA and protein in the viruses. -Phosphorus is found in DNA but not protein, and sulfur is found in protein but not DNA. -This was an elegant and simple way to determine what part of the virus entered the bacterium.
86
Diagram of the Hershey-Chase experiment
87
What did Hershey and Chase find through their experiment?
-When bacteriophages containing radioactive phosphorus (32 P) were allowed to infect nonradioactive bacteria, all the infected cells became radioactive. Additionally, the next generation of bacteriophages, produced from the infected bacteria, were all radioactive. -However, when the bacteria were infected with bacteriophages labelled with radioactive sulfur ( 35 S) and the virus coats removed (by agitating them in an electric blender), almost no radioactivity could be detected in the infected cells.
88
What did the findings of the Hershey-Chase experiment suggest?
-That the DNA component of the bacteriophages is injected into the bacterial cell, while the protein component remains outside. -Since the DNA entered the bacteria and caused the formation of radioactive bacteriophages, it showed that DNA was the genetic material.
89
Does DNA contain sulfur?
-No -DNA contains a lot of a phosphate, but no sulfur; while proteins contain sulfur (due to the two amino acids that contain sulfur, namely methionine and cysteine) but no phosphate.
90
In trying to determine whether DNA or protein is the genetic material, Hershey and Chase made use of which fact?
DNA contains phosphorus, whereas protein does not.
91
The results of the Hershey and Chase experiment support that the genetic material is ___
DNA
92
The diagram displays the setup of part of the Hershey–Chase experiment. Once the viruses have infected the bacterium, and they are destroyed and separated at the end of the experiment, where would you expect to find the radioactivity?
In the bacterium
93
How did solving the structure of DNA immediately suggest a mechanism for DNA replication?
-Double-stranded DNA has two complementary strands -Complementary base pairs form hydrogen bonds to connect each strand -If the two strands are separated, they each become a template to make an identical DNA molecule to the parent DNA molecule -This was immediately evident to Crick and Watson
94
What is the function of helicase in DNA replication?
-At the replication fork, helicase unwinds the double helix -Helicase breaks the hydrogen bonds between complementary base pairs and separates the strands -Each strand acts as a template
95
What is the function of single-stranded binding proteins in DNA replication?
They stabilize the single DNA strands until the new strand is made
96
What is the function of DNA gyrase in DNA replication?
-DNA gyrase moves ahead of helicase to support the unwinding of the DNA -Unwinding DNA causes the single-stranded DNA to coil up, increasing tension in the DNA molecule -DNA gyrase relieves this tension
97
What is the function of DNA primase in DNA replication?
-DNA primase adds a short RNA primer -This creates a short double-stranded region -The double-stranded region allows DNA polymerase III to bind -Only one RNA primer is made on the leading strand; multiple primers are made on the lagging strand
98
What is the function of free DNA nucleotides in DNA replication?
-They bind to exposed nucleotides on the template strands by complementary base pairing -Adenine binds with thymine and guanine with cytosine
99
What is the function of DNA polymerase III in DNA replication?
-It joins nucleotides in a 5' to 3' direction in the new strands -On the leading strand, DNA polymerase III follows the replication fork, connecting the sugar-phosphate backbone -On the lagging strand, DNA polymerase III moves away from the replication fork, forming Okazaki fragments
100
What is the function of DNA polymerase I in DNA replication?
-It removes each RNA primer and replaces it with DNA nucleotides -A gap between two nucleotides remains
101
What is the function of DNA ligase in DNA replication?
-Connects the sugar-phosphate backbone, filling the gap left by DNA polymerase I -This joins the multiple Okazaki fragments on the lagging strand
102
Give examples of non-coding regions of DNA that have important functions
-Introns -Telomeres -Genes for rRNA and tRNA -Controlling gene expression
103
What is the function of controlling gene expression?
-For example, the promoter region of a gene is not transcribed but it does regulate transcription -Proteins bind to these regions to enhance or repress transcription
104
What is the function of introns?
-The transcribed region of eukaryotic genes contains exons and introns -Introns are transcribed but are revived by splicing before the mRNA leaves the nucleus to be translated -Introns are involved in mRNA processing
105
What is the function of telomeres?
-Telomeres cap the ends of chromosomes -During each round of DNA replication, the ends of the chromosomes cannot be fully copied -This causes chromosomes to shorten with each replication -Telomeres protect the ends of chromosomes
106
What is the function of genes for rRNA and tRNA?
-Some RNA molecules are functional and are not translated -Ribosomal RNA (rRNA) is a part of ribosomes -Transfer RNA (tRNA) is involved in translation
107
What is the role of nucleosomes?
-Histones with the nucleosome help DNA to be packaged in the nucleus -Condensation of chromosomes is caused by nucleosomes associating together -This involves H1 and the interaction of tails of core histone proteins in adjacent nucleosomes -The condensation of DNA is called supercoiling -Nucleosomes and their modifications control the degree of DNA supercoiling
108
What is the structure of a bacteriophage?
It has a protein coat with DNA inside
109
What is the function of introns?
They are involved in mRNA processing

IB HL Biology (68 decks)

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