DNA Structure and Topology. Flashcards
1
Q
Define an autosome?
A
A chromosome that is not sex linked (humans have 22).
2
Q
Define a diploid cell?
A
A cell containing 2 complete sets of chromosomes (1 from each parent).
3
Q
Define the genome?
A
All of the genes that an organism possesses.
4
Q
Define haploid cells?
A
Also known as gametes, these cells only contain 1 set of chromosomes.
5
Q
Define the nuclear genome?
A
The nuclear genome refers to the DNA that is found on the chromosomes, within the nucleus of the cell.
6
Q
Define the proteome?
A
A cells repertoire of proteins which are formed via translation.
7
Q
Define a pyrophosphate molecule?
A
2 phosphate molecules that are joined together.
8
Q
Define somatic cells?
A
Any cell within the body that is not a reproductive cell. Somatic cells are diploid.
9
Q
Define the transcriptome?
A
The transcriptome consists of the RNA copies of protein coding genes and have been made via DNA transcription.
10
Q
What is the human genome also known as?
A
The nuclear genome.
11
Q
How many nucleotides are found in the human genome?
A
3.2 billion nucleotides.
12
Q
How many pairs of autosomes are found in the human genome?
A
22.
13
Q
How many sex chromosomes are found in the human genome?
A
2.
14
Q
How many genes are found in the human genome?
A
Approx 25,000 genes.
15
Q
Is the nuclear genome the only genome to be found in the human cell?
A
No.
Mitochondria also have a genome.
16
Q
What are the 3 characteristics of MtDNA?
A
Circular in shape.
16,569 base pairs.
37 genes.
17
Q
Can mitochondrial genes suffer from mutations?
A
Yes. And these mutations can lead to mitochondrial disorders.
18
Q
Will the nuclear and mitochondrial genome be found in all of the cells within the body?
A
Yes.
19
Q
What are the 2 types of cells that are found in the human body?
A
Somatic cells (diploid).
Sex cells or gametes (haploid).
20
Q
An organisms genome contains the information needed for what processes?
A
To construct and maintain a living organism.
21
Q
DNA is responsible for what?
A
For storing hereditary information in a stable manner.
And for encoding information for various characteristics such as the manufacturing of proteins.
22
Q
What does DNA do during cell division?
A
It will accurately replicate itself so that the new cell also contains genetic information.
23
Q
What will arise if DNA does not replicate itself accurately?
A
Mutations can arise which can lead to genetic disease.
24
Q
What processes have been helped by genetic mutations?
A
Evolution.
25
What 2 processes can DNA be said to regulate?
Its own expression.
Evolution.
26
What information allows the body to make proteins?
Genetic information.
27
What process leads to the formation of DNA?
DNA replication.
28
What information is stored in DNA?
Hereditary information
Information for protein manufacture.
29
What process must DNA first undergo for proteins to be made from DNA?
DNA must undergo transcription (also known as genome expression) and be transcribed to a specific piece of RNA.
30
What kind of RNA is DNA transcribed to?
mRNA.
31
Where does protein manufacturing occur?
In the ribosomes.
32
Why must DNA be transcribed to RNA for protein manufacture to take place?
Because DNA cannot leave the nucleus, so the mRNA acts as a messenger.
33
What happens to the mRNA molecule after it has travelled to the ribosomes?
It will undergo translation (also known as transcriptome expression) and be translated into a protein.
34
What is the central dogma of genetics and molecular biology?
The process of DNA to mRNA to protein.
35
What process is used to make DNA from RNA?
Reverse transcription and this process occurs in some viruses.
36
Who is often referred to as the father of genetics?
Gregor Mendel.
37
What did Mendel determine from his research on pea plants?
He discovered that heritable factors or unit factors were transmitted form parent to offspring and that many of these factors separated during gametogenesis.
38
How did Mendel perform his pea plant experiments?
He would try to produce certain characteristics in the offspring of pea plants.
E.g. He would cross a purple flower with a white flower and try to produce an offspring with pink flower.
39
What are Mendels unit factors now known as?
Alleles.
40
Did Mendel create a pink plant when he crossed a white and pink flower?
No, all the offspring were white.
However, when the offspring was allowed to self pollinate purple offspring were produced meaning that even though the purple colour wasn’t displayed in the parental flower, it was still transmitted from its grandparents.
41
The inheritance of alleles is known as what kind of inheritance?
Mendelian inheritance.
42
The expression of different flower colours in the different generations of Mendels pea plant experiments is due to what?
Alleles.
43
What does Mendels law of segregation explain?
That the alleles of 2 or more different genes are sorted into gametes independently of each other.
This means that the allele that a gamete receives for 1 gene will not influence the allele received for another.
44
Who coined the word gene and when?
Wilhelm Johanssen in 1909.
45
What kind of cross can prove some of the principles in the law of segregation and Mendelian inheritance?
A monohybrid cross.
46
Who isolated a substance that he called nuclein from the white blood cells of wounded soldiers and from salmon sperm and when did he do it?
Johann Mischer in 1869 .
47
What 2 atoms are were high in the nuclein that Miescher found?
Phosphorous and nitrogen.
48
What do we call the nuclein that Miescher found?
Nucelic acid.
49
What molecule did most people think was the hereditary material before DNA was discovered?
Proteins.
50
When did Fredrick Griffiths conduct his experiment?
1927.
51
What strains of bacteria did Fredrick Griffiths use in his experiment?
2 different strains of streptococcus pneumoniae bacteria.
A rough strain that was nonvirulent.
A smooth strain that was virulent.
52
What happened when Griffiths injected mice with the smooth strain of bacteria?
They died.
53
What happened when Griffiths injected mice with the rough strain of bacteria?
They were unaffected.
54
What was the virulence factor that the S strain of bacteria had in Griffiths experiment?
A capsule.
55
What happened when Griffith used heat to kill the S strain and then re-injected them into the mice?
The mice survived.
56
What happened when Griffith mixed the heat killed S strain with the nonvirulent R strain and then injected the mixture into the mice?
The mice died.
57
What did Griffith believe had been passed between the heat killed S strain and the rough strain which allowed the rough strain to transform and affect the mice?
Griffiths believed that proteins had been transferred between the 2 strains of bacteria to induce the transformation.
58
When did the Avery, McLeod and McCarty experiment take place?
In 1944.
59
What was the aim of Avery, McLeod and McCarty's experiment?
To try and identify the component that caused the transformation in Griffiths experiment.
60
How did Avery, McLeod and McCarty conduct their experiment?
They took a large amount of heat killed S cells and divided them into 3 categories.
61
What was removed from the 1st of the 3 categories of heat killed cells used in Avery, McLeod and McCarty's experiment?
The first category had been treated with a ribonuclease to remove of the RNA.
62
What happened when the 1st category of cells were mixed with R cells and injected into a mouse in Avery, McLeod and McCarty's experiment?
The mouse died.
63
What was removed from the 2nd of the 3 categories of heat killed cells used in Avery, McLeod and McCarty's experiment?
The second group of S cells had been treated with a protease to remove all of the proteins from them.
64
What happened when the 2nd category of cells were mixed with S cells and injected into a mouse in Avery, McLeod and McCarty's experiment?
The mouse died.
65
Why were the RNA and proteins were not responsible for the transformation in bacteria in Avery, McLeod and McCarty's experiment?
As the R strain had managed to pick up the virulence factor.
66
What was removed from the 3rd of the 3 categories of heat killed cells used in Avery, McLeod and McCarty's experiment?
The final group of S cells had been treated with a deoxyribonuclease to remove all of the the DNA.
67
What happened when the 3rd category of cells were mixed with S cells and injected into a mouse in Avery, McLeod and McCarty's experiment?
The mouse survived.
This gave very strong evidence that DNA was the transforming factor in Griffiths experiment.
68
When did the Hershey Chase experiment take place?
In 1952.
69
What was the aim of the Hershey Chase experiment?
To find out whether bacteriophages injected DNA or proteins into bacteria when they attacked them.
70
How did Hershey and Chase set up their experiment?
They took a number of bacteriophages and divided them into 2 categories by injecting a radioactive isotope of sulphur to one group and a radioactive isotope of phosphorous to the other.
71
Why did Hershey and Chase inject radioactive sulphur into the one group of bacteriophages?
Sulphur is found in many proteins and is not found in DNA, so only proteins would receive the sulphur isotope.
72
Why did Hershey and Chase inject radioactive phosphorous into the one group of bacteriophages?
Phosphorous is present in DNA and not found in proteins.
This means that if DNA were the hereditary material then the phosphorous would be found in the infected bacteria.
73
What happened to the 2 groups of bacteria after they had been injected by phages in the Hershey Chase experiment?
They were blended to remove any phage parts from the outside of the bacteria.
The blended remains centrifuged which separated the bacteria from any phage parts.
74
What happened when the bacteria were removed from the centrifuge and analysed in the Hershey Chase experiment?
A higher percentage of radioactive phosphorous was found in the bacteria.
75
Why did the Hershey Chase experiment prove that DNA was the hereditary material?
The high percentage of radioactive phosphorous found in the bacteria had been transferred from the phage to the bacteria.
The radioactive sulphur was found in the phage parts and had not been transferred.
76
Who discovered the 4 bases in DNA and found that they have specific pairings?
Erwinn Chagraff
77
What are the 4 nucleotides that DNA is composed of?
Adenine.
Guanine.
Cytosine.
Thymine.
78
Of the 4 nucleotides found in DNA, which ones are pyrimidines?
PYCT.
Cytosine.
Thymine.
79
Of the 4 nucleotides found in DNA, which ones are purines?
PUR AG.
Adenine.
Guanine.
80
What base will adenine always pair with?
Adenine always pairs with thymine.
81
What base will guanine always pair with?
Guanine always pairs with cytosine.
82
How did Chagraff came up with his theory of base pairing?
He extracted and purified DNA.
He use acid hydrolysis to break to release the nucleotides.
He then quantified the nucleotides by chromatography.
83
What did Chagraff discover about the amounts of DNA bases in different species?
That the amounts of the bases in DNA differs from species to species.
84
Are the base pairs in a DNA strand represented equally?
No.
Only the base pairs in equal amounts.
E.g. If a section of DNA is 20% thymine, then it will be 20% adenine.
85
What is the equation for the base pairs in a DNA strand?
A=T.
C=G.
86
A section of DNA consists of 29% guanine, how much thymine would be in the same section?
Total % of pyrimidines = 100 - total % of purines.
% of pyrimidines = 100 - 58 = 42.
Total % of thymine = 42/2 = 21.
Therefore, Purines.
Adenine = 29%.
Guanine = 29%.
Pyrimidines.
Cytosine = 21%.
Thymine = 21%.
87
Who discovered the structure of DNA?
Rosalind Franklin.
James Watson.
Maurice Wilkins.
Francis Crick.
88
What was Rosa Franklins contribution to the discover of DNA?
She performed X-ray crystallography on a DNA molecule.
This gave clues to the symmetry, consistency and dimensions of DNA.
89
What data did Watson and Crick use to come up with their double helix model of DNA?
Chagraff's base ratios.
Biophysical data.
Scale model building.
90
What kind of molecule is DNA?
A polynucleotide (polymer of nucleotides).
91
How many rings do purines have?
Purines have 2 ringed structures.
92
How many rings do purines pyrimidines have?
Pyrimidines have 1 ring structures.
93
What is a nucleotide made up of?
A 4 carbon sugar called a deoxyribose.
A phosphate group.
A base.
94
What sugar is found in the nucleotides of DNA?
Deoxyribose.
95
What end of the DNA molecule is the phosphate group found on?
The 5 prime end.
96
What does the phosphate group on the 5 prime end of DNA consist of?
It consists of 3 phosphates which are known as alpha, beta and gamma.
97
How many phosphate groups are on the phosphates that are not at the 5 prime end?
They have 1 phosphate attached to them.
98
Which phosphate attaches to the carbon?
The 5 prime end of the alpha phosphate attaches to carbon 4 of the sugar molecule.
99
What is the difference between a nucleotide and a nucleoside?
A nucleoside is a nucleotide with no phosphates.
100
How can you recognise the 5 prime end of a DNA polymer?
By the presence of a nucleotide triphosphate.
101
How can you recognise the 3 prime end of a DNA polymer?
It will always have a hydroxyl group.
102
What carbon on the sugar does the hydroxyl group bind to?
Carbon 3.
103
What bonds link the nucleotides in the DNA polymer?
Phosphodiester bonds.
104
What 3 steps lead to phosphodiester bonds formation?
DNA polymerase cleaves 2 phosphates from the nucleotide that is being attached.
The nucleotide monophosphate is attached to the hydroxyl group on carbon 3 of the 1st nucleotide.
This process will occur again and again to make the molecule longer and longer.
105
What enzyme will attach the nucleotides together in a DNA strand?
DNA polymerase.
106
Is DNA double or single stranded?
Double stranded.
107
How are the 2 nucleotide stands that make up DNA arranged?
They are antiparallel, meaning that 1 strand runs from 5 prime to 3 prime and the other runs from 3 prime to 5 prime.
108
What bonds will hold the 2 strands of nucleotides together?
Hydrogen bonds.
109
Where are the hydrogen bonds formed in the DNA molecule?
Between the base pairs (A and T or C and G).
110
How many hydrogen bonds are formed between cytosine and guanine?
3 hydrogen bonds.
111
How many hydrogen bonds are formed between adenine and thymine?
2 hydrogen bonds.
112
A DNA strand containing a lot of what nucleotides will be harder to prise apart?
A sequence that contains a lot of Gs and Cs is much stronger than the same sequence with As and Ts.
113
What is the structure of the DNA strand?
It forms a ladder like structure with phosphodiester sides and base pair rungs.
The ladder will twist to form a spiral staircase structure or an alpha helix.
114
What are the 3 different conformations that DNA can take up while in the alpha helix?
B DNA.
A DNA.
Z DNA.
115
What type of DNA makes up B DNA?
Chromosomal DNA.
116
What is the structure of B DNA?
It will form right handed turns with 10 base pairs per complete turn.
117
What is A DNA?
DNA that is slightly dehydrated.
118
What kind of turns will DNA always form?
Right handed turns.
119
How many base pairs per turn will A DNA have?
11 base pairs per complete turn.
120
Where will Z DNA be found?
In regions of DNA that have alternating purines and pyrimidines e.g. GCGCGC or ATATAT.
121
Transitions between what forms of DNA are thought to play a role in regulating gene expression?
Transitions between the B and the Z form.
122
Why do B and Z DNA transition between the 2 forms?
Because Z DNA is easier to read than B DNA so there is a transition between the 2 when genes are being expressed.
123
What is the only conformation of DNA that forms left handed turns?
Z DNA and it has 12 base pairs per complete turn.
124
What kind of DNA packaging is used in prokaryotes?
Supercoiling.
125
Do prokaryotes have a nucleus?
No.
126
What is the purpose of supercoiling?
To allow the DNA molecule to fit into the cell.
127
Where is DNA stored in prokaryotes?
In the nucleoid region of the cytoplasm.
128
Where will eukaryotes store their DNA?
In the nucleus on specific structures called chromosomes.
129
What for of DNA in eukaryotes is supercoiled?
Mitochondrial DNA.
130
Is DNA in prokaryotes double stranded?
Yes.
131
What is the prokaryotic genome shaped like?
A large closed circle.
132
What proteins will help fold and condense prokaryotic DNA to allow it to fit into the cell?
HU proteins.
133
How are supercoils formed?
DNA strands coil around themselves to form secondary coils which are known as supercoils.
134
What are the 2 types of supercoil?
Negative and positive supercoils.
135
What state is prokaryotic DNA in when it is being transcribed
A relaxed state.
136
What enzymes help regulate the level of supercoiling?
Enzymes called topoisomerases.
137
How do topoisomerases regulate the level of supercoiling during transcription?
Topisomerases cuts a strand of DNA, allowing the DNA strand to be opened up.
When transcription is finished, the topoisomerase will seal the cut allowing supercoil to reform.
138
How will intercalators affect supercoiling?
They can alter the geometry of supercoils.
139
What is a good example of an intercalator?
Ethidium bromide.
It is positively charged and can insert itself between base pairs which causes the DNA to unwind in that area.
140
What structures is eukaryotic DNA stored on?
Chromosomes.
141
Where are chromosomes found?
In the nuclei of cells.
142
What is the first step of eukaryotic DNA storage?
To wind the double stranded DNA around positively charged proteins called histones.
143
What is the histone core made up of?
It is made up of 4 pairs of protein monomers called H2A, H2B, H3 and H4.
144
What is the histone core also known as?
An octamer.
145
What is formed when DNA has wrapped around multiple histones?
A nucleosome which is said to resemble beads on a string.
146
What is core particle of a nucleosome?
A histone octamer and around 146 base pairs of DNA.
147
What makes up the part of a nucleosome that isn't in the core particle?
Linker DNA which is around 54 base pairs and links the histones together.
148
What is the job of histone H1 in the nucleosome?
It binds the nucleosome together by holding the core particle and linker DNA together.
149
How are nucleosomes packaged onto chromosomes?
They condense to form a structure called a solenoid.
The solenoid is compacted into chromatin loops.
The chromatin loops coil up to form chromatids that are found in chromosomes.
