2.1.3 - Nucleotides and nucleic acids Flashcards
(100 cards)
1
Q
What does DNA stand for ?
A
Deoxyribonucleic acid
2
Q
What does RNA stand for ?
A
Ribonucleic acid
3
Q
What are the monomeric unit for nucleic acids ?
A
- Nucleotides
4
Q
What are the 3 components of a nucleotide?
A
- Phosphate group
- Pentose sugar, either deoxyribose or ribose
- Nitrogenous base
5
Q
Name the 5 nitrogenous bases
A
- thymine
- guanine
- adenine
- cytosine
- uracil
6
Q
Name the 4 bases present in DNA
A
- thymine
- adenine
- guanine
- cytosine
7
Q
Which base is never found in DNA ?
A
Uracil
8
Q
Which base is never found in RNA ?
A
Thymine
9
Q
How are polynucleotides formed ?
A
- Condensation reactions occur
- The reaction occurs between the phosphate on carbon 5 of one nucleotide and the hydroxyl group on carbon 3 of another nucleotide
- Water is released
10
Q
What sort of bond is formed between nucleotides?
A
Phosphodiester
11
Q
What are the two types of bases ?
A
Purines and Pyrimidines
12
Q
What is the structure of pyrimidines?
A
They only have one carbon ring
13
Q
Which bases are pyrimidines ?
A
- Cytosine
- Thymine
- Uracil
14
Q
What is the structure of purines?
A
They have two carbon rings
15
Q
Which bases are purines ?
A
- Adenine
- Guanine
16
Q
What type of bonds hold bases together ?
A
Hydrogen bonds
17
Q
How many hydrogen bonds form between Adenine and Uracil/Thymine ?
A
2 hydrogen bonds
18
Q
How many hydrogen bonds form between Guanine and Cytosine?
A
3 hydrogen bonds
19
Q
Describe the steps involved in extracting DNA
A
- The sample is ground up using pestle and mortar
- Sample mixed with detergent
- Salt is added
- Protease is added
- Ice cold ethanol is added down the side of the test tube
20
Q
Why is the sample ground in the extraction of DNA ?
A
This is to break down the cell walls
21
Q
Why is detergent added to the sample in the extraction of DNA ?
A
This breaks down the cell membranes, releasing the cell contents into solution
22
Q
Why is salt added to the sample in the extraction of DNA ?
A
- The salt neutralises the charges on phosphates in the sugar phosphate backbone
- It breaks down the hydrogen bonds between DNA and water molecules
- Makes the DNA less soluble
23
Q
Why is protease added to the sample in the extraction of DNA ?
A
It breaks down the histone proteins that are associate with DNA
24
Q
Why is ethanol added to the sample in the extraction of DNA ?
A
It causes the DNA to form a white precipitate between the layer of the sample and the ethanol
25
Why is a low temperature maintained throughout the process of DNA extraction ?
This reduces the rate of enzyme controlled reactions that break down the DNA
26
Why should the ethanol be ice cold ?
It helps to make the DNA more insoluble
27
Outline how DNA is replicated
- DNA helicase unwinds DNA from histones and unzips DNA by breaking hydrogen bonds between complementary base pairs
- Free nucleotides are attracted to the exposed nucleotides on the strand of DNA by base complementarity
- DNA polymerase forms phosphodiester bonds between nucleotides
- Two genetically identical molecules of DNA are formed
28
At what point in the cell cycle does DNA replication occur ?
S phase
29
Why is it important that DNA replication results in 2 genetically identical molecules of DNA ?
- Ensures the continuation of species
| - Ensures cells and structures in a species are maintained
30
Why is DNA replication described as being semi-conservative ?
- Each one of the two daughter molecules contains one original strand of DNA and one newly synthesised strand
- The original strand acts as a template for a new strand
31
What is the relationship between the two daughter molecules ?
They are genetically identical
32
What is the relationship between the daughter molecules and the original DNA molecule ?
They are identical
33
Which two enzymes are used in DNA replication ?
- DNA helicase
| - DNA polymerase
34
What is the role of DNA helicase ?
- Unwinds DNA from histones proteins
| - It does this by breaking hydrogen bonds between complementary base pairs
35
What is the role of DNA polymerase ?
Catalyses the reaction to form phosphodiester bonds between the free nucleotides to form a sugar phosphate backbones
36
What does the unzipping mean for DNA nucleotides ?
They are exposed
37
Due to the nucleotides being exposed, what happens ?
Free nucleotides are attracted to the exposed nucleotides by base complementarity and form hydrogen bonds
38
Where do the free nucleotides come from ?
- Exogenous, come from our diet.
| - We can also synthesise nucleotides.
39
How do free nucleotides enter the nucleus ?
From the cytoplasm through the nuclear pores
40
What is a primer ?
A short piece of RNA or DNA with a complementary sequence to part of the DNA template
41
Why are primers needed in DNA replication ?
DNA polymerase requires them in order to bond to the 3' OH group
42
What direction does DNA synthesis occur ?
5' to 3'
43
What is the difference between the leading strand and lagging strand ?
The leading strand is built continuously whereas the lagging strand is built discontinuously
44
Why is there a leading strand and a lagging strand ?
The antiparallel nature of DNA
45
What does the discontinuous building of the lagging strand lead to the production of ?
Okazaki fragments
46
Which experiment was used to prove that DNA replication is semi-conservative ?
The Meselsohn and Stahl experiment
47
What was the key experiment in the Meselsohn and Stahl experiments ?
- E.coli was grown in a growth media containing N-15 for several divisions
- it was then transferred to a growth media containing N-14 and only allowed to divide once
- the DNA was then extracted and centrifuged with CsCl
48
Which two techniques did the Meselsohn and Stahl experiment use ?
- Mass labelling
| - Density centrifugation
49
Which isotope was used for mass labelling in the Meselsohn and Stahl experiment ?
N-15
50
Why was N-15 used in the Meselsohn and Stahl experiment ?
It could be incorporated into the nitrogenous bases and therefore track the movement of them
51
Which part of the nucleotide was labelled in mass labelling ?
The nitrogenous bases
52
How did density centrifugation work in the Meselsohn and Stahl experiment ?
- A CsCl gradient is produced by centrifugation
- More dense molecules move to the bottom and lighter molecules to the top
- When DNA is placed into this solution it migrates to the position in the gradient with the same buoyant density
53
DNA was placed in a solution of what in the Meselsohn and Stahl experiment ?
CsCl (caesium chloride)
54
Outline the two control experiments in the Meselsohn and Stahl experiment
- E.coli placed in growth factor containing N-15 (heavy nitrogen) which the E.coli incorporated into their DNA, DNA extracted and centrifuged with CsCl
- E.coli placed in growth factor containing N-14 (normal nitrogen) which the E.coli incorporated into their DNA, DNA extracted and centrifuged with CsCl
55
What was seen in the two control experiments in the Meselsohn and Stahl experiment ?
N-15, the DNA settled further down the density gradient whilst the N-14 DNA was higher up the density gradient
56
Why was E.coli used in the Meselsohn and Stahl experiment ?
- the environment in which it grows can be carefully controlled
- It would incorporate the different isotopes of Nitrogen into its DNA
- It divides every 20 minutes
57
Why were the control experiments important to the Meselsohn and Stahl experiment ?
- They allowed the position of where each N isotope sits after centrifugation depending on its density to be identified
- If there was a mixing of the two isotopes a band would be seen in between
58
What was observed in the key Meselsohn and Stahl experiment ?
A band of DNA was formed in between the N-15 and N-14 bands
59
How did the key Meselsohn and Stahl experiment prove DNA replication is semi-conservative ?
- The initial molecule of DNA contained only N-15 nucleotides
- As DNA replication is semi-conservative the DNA which was newly synthesised in the N-14 growth media would contain one strand with N-15 nucleotides and one strand with N-14 nucleotides
- So the band would be in the middle
60
Suggest 3 precautions that Meselson and Stahl would have taken in order to ensure that the centrifugation part of their investigation produced valid results
- The tubes were spun for the same amount of time
- The tubes were spun at the same speed
- The solution the DNA is put in is the same concentration
61
What are the differences between RNA and DNA ?
- RNA has a ribose sugar, DNA has a deoxyribose sugar
- RNA has one strand whereas DNA has two strands
- RNA has Uracil whereas DNA has Thymine instead
62
What are some similarities between RNA and DNA ?
- Both have Purines and Pyrimidines
- Both of them form hydrogen bonds
- Both have purines bonding with pyrimidines
63
Where does protein synthesis occur ?
Protein synthesis occurs at ribosomes
64
What is the sense strand ?
- The strand that contains the code for the protein to be synthesised
- Runs from 5' to 3'
65
What is the antisense strand ?
- A complementary copy of the sense strand, does not code for a protein
- runs from 3' to 5'
66
What does the antisense strand act as ?
- It acts as the template strand
| - The complementary RNA strand formed carries the same base sequence as the sense strand
67
What is RNA polymerase ?
RNA polymerase forms the phosphodiester bonds between the RNA nucleotides
68
What is mRNA ?
- messenger RNA, leaves the nucleus via nuclear pores to go to the ribosomes
- This is the complete short strand of DNA
69
What is the base sequence like in mRNA ?
Uracil bonds to Adenine instead of Thymine
70
What is rRNA ?
- ribosomal RNA, makes up ribosomes
- They are important in maintaining the structural stability of the protein synthesis sequence and plays a role in catalysing the reaction
71
What happens after the mRNA leaves the nucleus ?
- The mRNA binds to a specific site on the small subunit of a ribosome
- The ribosome holds mRNA in position while it is decoded into a sequence of amino acids
72
What is this process called ?
Translation
73
What is tRNA ?
transfer RNA is necessary for the translation of mRNA
74
What is tRNA composed of ?
It is composed of a strand of RNA folded in such a way that three bases, the anticodon, are at one end of the molecule. There is an amino acid at the other end
75
What does the anticodon bind to ?
Binds to a complementary codon on mRNA following the normal base pairing rules
76
What does tRNA carry ?
The tRNA molecules carry an amino acid corresponding to that codon
77
What is the role of ribosomes ?
Ribosomes act as the bonding site for mRNA and tRNA and catalyse the assembly of the protein
78
How does the protein grow ?
Amino acids are added one at a time and the protein grows as this happens
79
When does translation come to an end ?
When a stop codon is reached and the polypeptide is released
80
What could happen at the golgi apparatus ?
The protein may undergo further modification before it is fully functional and ready to carry out the specific role for which it has been synthesised
81
In what forms does energy come ?
- Heat
- Light
- In chemical bonds
82
Why do cells require energy ?
- Synthesis - of large molecules such as proteins
- Transport - pumping molecules or ions across cell membranes by active transport
- Movement - protein fibres in muscle cells that cause muscle contractions
83
What is ATP composed of ?
- Adenine base
- A ribose sugar
- Three phosphate groups
84
What does ATP stand for ?
Adenosine triphosphate
85
How is ATP created ?
The energy released in the breakdown of fats and carbs is used to create ATP
86
What is the transfer of energy like in ATP ?
A small amount of energy is needed to break the bond holding that last phosphate group. However, a large amount of energy is then released when the liberated phosphate undergoes other bond forming reactions.
87
What type of reaction is the removal of the third phosphate group ?
Hydrolysis reaction as water is added to remove it
88
What is the equation for the removal of the third phosphate group ?
- ATP + H2O —> ADP + Pi + energy
| - Pi is the inorganic phosphate that has been released
89
What is ATP hydrolysed to ?
- Adenosine Diphosphate
- Phosphate ion
- Energy
90
Why is ATP not a good long term energy store ?
- The bonds between the phosphate groups in ATP are unstable
| - Carbs and fats are a lot better for this
91
Why is it unstable ?
The three phosphate groups repel each other due to the fact that they are all negatively charged.
92
What are the advantages of ATP ?
- Instant source of energy in the cell
- Releases energy in small amounts as needed
- It is mobile and transports chemical energy where it is needed in the cell
- Universal energy carrier and can be used in many different reactions
93
What are the properties of ATP ?
- Small - moves easily in, out and within cells
- Water soluble - energy requiring process can happen in aqueous environments
- Contains bonds between phosphates with intermediate energy - Large enough to be useful for cellular reactions but not so large that energy is wasted as heat
- Releases energy in small quantities - Energy is not wasted as heat
- Easily regenerated - Can be recharged with energy
94
Why is ATP better than glucose ?
- The energy released from the splitting of ATP into ADP releases energy in small, manageable bursts
- Hydrolysis of ATP to ADP is a single reaction, glucose breakdown requires a long series of reactions
95
What is phosphorylation ?
Phosphorylation is making ATP by adding a phosphate ion on
96
What type of reaction is this ?
Condensation reaction as water is removed in this process
97
What are the three types of phosphorylation ?
- Photophosphorylation
- Oxidative phosphorylation
- Substrate-level phosphorylation
98
What is Photophosphorylation ?
Occurs in the chlorophyll during photosynthesis
99
What is Oxidative phosphorylation ?
Occurs in the mitochondria during the electron transport chain ( part of respiration )
100
What is Substrate-level phosphorylation ?
When phosphate groups are transferred from donor molecules to ADP
