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Biology > 2.1.3 - Nucleotides and nucleic acids > Flashcards

2.1.3 - Nucleotides and nucleic acids Flashcards

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1
Q

What does DNA stand for ?

A

Deoxyribonucleic acid

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2
Q

What does RNA stand for ?

A

Ribonucleic acid

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3
Q

What are the monomeric unit for nucleic acids ?

A
  • Nucleotides
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4
Q

What are the 3 components of a nucleotide?

A
  • Phosphate group
  • Pentose sugar, either deoxyribose or ribose
  • Nitrogenous base
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5
Q

Name the 5 nitrogenous bases

A
  • thymine
  • guanine
  • adenine
  • cytosine
  • uracil
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6
Q

Name the 4 bases present in DNA

A
  • thymine
  • adenine
  • guanine
  • cytosine
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7
Q

Which base is never found in DNA ?

A

Uracil

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8
Q

Which base is never found in RNA ?

A

Thymine

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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
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10
Q

What sort of bond is formed between nucleotides?

A

Phosphodiester

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11
Q

What are the two types of bases ?

A

Purines and Pyrimidines

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12
Q

What is the structure of pyrimidines?

A

They only have one carbon ring

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13
Q

Which bases are pyrimidines ?

A
  • Cytosine
  • Thymine
  • Uracil
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14
Q

What is the structure of purines?

A

They have two carbon rings

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15
Q

Which bases are purines ?

A
  • Adenine

- Guanine

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16
Q

What type of bonds hold bases together ?

A

Hydrogen bonds

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17
Q

How many hydrogen bonds form between Adenine and Uracil/Thymine ?

A

2 hydrogen bonds

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18
Q

How many hydrogen bonds form between Guanine and Cytosine?

A

3 hydrogen bonds

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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
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20
Q

Why is the sample ground in the extraction of DNA ?

A

This is to break down the cell walls

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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

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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
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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

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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

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25
Q

Why is a low temperature maintained throughout the process of DNA extraction ?

A

This reduces the rate of enzyme controlled reactions that break down the DNA

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26
Q

Why should the ethanol be ice cold ?

A

It helps to make the DNA more insoluble

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27
Q

Outline how DNA is replicated

A
  • 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
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28
Q

At what point in the cell cycle does DNA replication occur ?

A

S phase

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29
Q

Why is it important that DNA replication results in 2 genetically identical molecules of DNA ?

A
  • Ensures the continuation of species

- Ensures cells and structures in a species are maintained

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30
Q

Why is DNA replication described as being semi-conservative ?

A
  • 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
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31
Q

What is the relationship between the two daughter molecules ?

A

They are genetically identical

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32
Q

What is the relationship between the daughter molecules and the original DNA molecule ?

A

They are identical

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33
Q

Which two enzymes are used in DNA replication ?

A
  • DNA helicase

- DNA polymerase

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34
Q

What is the role of DNA helicase ?

A
  • Unwinds DNA from histones proteins

- It does this by breaking hydrogen bonds between complementary base pairs

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35
Q

What is the role of DNA polymerase ?

A

Catalyses the reaction to form phosphodiester bonds between the free nucleotides to form a sugar phosphate backbones

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36
Q

What does the unzipping mean for DNA nucleotides ?

A

They are exposed

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37
Q

Due to the nucleotides being exposed, what happens ?

A

Free nucleotides are attracted to the exposed nucleotides by base complementarity and form hydrogen bonds

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38
Q

Where do the free nucleotides come from ?

A
  • Exogenous, come from our diet.

- We can also synthesise nucleotides.

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39
Q

How do free nucleotides enter the nucleus ?

A

From the cytoplasm through the nuclear pores

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40
Q

What is a primer ?

A

A short piece of RNA or DNA with a complementary sequence to part of the DNA template

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41
Q

Why are primers needed in DNA replication ?

A

DNA polymerase requires them in order to bond to the 3’ OH group

42
Q

What direction does DNA synthesis occur ?

A

5’ to 3’

43
Q

What is the difference between the leading strand and lagging strand ?

A

The leading strand is built continuously whereas the lagging strand is built discontinuously

44
Q

Why is there a leading strand and a lagging strand ?

A

The antiparallel nature of DNA

45
Q

What does the discontinuous building of the lagging strand lead to the production of ?

A

Okazaki fragments

46
Q

Which experiment was used to prove that DNA replication is semi-conservative ?

A

The Meselsohn and Stahl experiment

47
Q

What was the key experiment in the Meselsohn and Stahl experiments ?

A
  • 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
Q

Which two techniques did the Meselsohn and Stahl experiment use ?

A
  • Mass labelling

- Density centrifugation

49
Q

Which isotope was used for mass labelling in the Meselsohn and Stahl experiment ?

A

N-15

50
Q

Why was N-15 used in the Meselsohn and Stahl experiment ?

A

It could be incorporated into the nitrogenous bases and therefore track the movement of them

51
Q

Which part of the nucleotide was labelled in mass labelling ?

A

The nitrogenous bases

52
Q

How did density centrifugation work in the Meselsohn and Stahl experiment ?

A
  • 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
Q

DNA was placed in a solution of what in the Meselsohn and Stahl experiment ?

A

CsCl (caesium chloride)

54
Q

Outline the two control experiments in the Meselsohn and Stahl experiment

A
  • 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
Q

What was seen in the two control experiments in the Meselsohn and Stahl experiment ?

A

N-15, the DNA settled further down the density gradient whilst the N-14 DNA was higher up the density gradient

56
Q

Why was E.coli used in the Meselsohn and Stahl experiment ?

A
  • 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
Q

Why were the control experiments important to the Meselsohn and Stahl experiment ?

A
  • 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
Q

What was observed in the key Meselsohn and Stahl experiment ?

A

A band of DNA was formed in between the N-15 and N-14 bands

59
Q

How did the key Meselsohn and Stahl experiment prove DNA replication is semi-conservative ?

A
  • 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
Q

Suggest 3 precautions that Meselson and Stahl would have taken in order to ensure that the centrifugation part of their investigation produced valid results

A
  • 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
Q

What are the differences between RNA and DNA ?

A
  • 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
Q

What are some similarities between RNA and DNA ?

A
  • Both have Purines and Pyrimidines
  • Both of them form hydrogen bonds
  • Both have purines bonding with pyrimidines
63
Q

Where does protein synthesis occur ?

A

Protein synthesis occurs at ribosomes

64
Q

What is the sense strand ?

A
  • The strand that contains the code for the protein to be synthesised
  • Runs from 5’ to 3’
65
Q

What is the antisense strand ?

A
  • A complementary copy of the sense strand, does not code for a protein
  • runs from 3’ to 5’
66
Q

What does the antisense strand act as ?

A
  • It acts as the template strand

- The complementary RNA strand formed carries the same base sequence as the sense strand

67
Q

What is RNA polymerase ?

A

RNA polymerase forms the phosphodiester bonds between the RNA nucleotides

68
Q

What is mRNA ?

A
  • messenger RNA, leaves the nucleus via nuclear pores to go to the ribosomes
  • This is the complete short strand of DNA
69
Q

What is the base sequence like in mRNA ?

A

Uracil bonds to Adenine instead of Thymine

70
Q

What is rRNA ?

A
  • 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
Q

What happens after the mRNA leaves the nucleus ?

A
  • 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
Q

What is this process called ?

A

Translation

73
Q

What is tRNA ?

A

transfer RNA is necessary for the translation of mRNA

74
Q

What is tRNA composed of ?

A

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
Q

What does the anticodon bind to ?

A

Binds to a complementary codon on mRNA following the normal base pairing rules

76
Q

What does tRNA carry ?

A

The tRNA molecules carry an amino acid corresponding to that codon

77
Q

What is the role of ribosomes ?

A

Ribosomes act as the bonding site for mRNA and tRNA and catalyse the assembly of the protein

78
Q

How does the protein grow ?

A

Amino acids are added one at a time and the protein grows as this happens

79
Q

When does translation come to an end ?

A

When a stop codon is reached and the polypeptide is released

80
Q

What could happen at the golgi apparatus ?

A

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
Q

In what forms does energy come ?

A
  • Heat
  • Light
  • In chemical bonds
82
Q

Why do cells require energy ?

A
  • 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
Q

What is ATP composed of ?

A
  • Adenine base
  • A ribose sugar
  • Three phosphate groups
84
Q

What does ATP stand for ?

A

Adenosine triphosphate

85
Q

How is ATP created ?

A

The energy released in the breakdown of fats and carbs is used to create ATP

86
Q

What is the transfer of energy like in ATP ?

A

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
Q

What type of reaction is the removal of the third phosphate group ?

A

Hydrolysis reaction as water is added to remove it

88
Q

What is the equation for the removal of the third phosphate group ?

A
  • ATP + H2O —> ADP + Pi + energy

- Pi is the inorganic phosphate that has been released

89
Q

What is ATP hydrolysed to ?

A
  • Adenosine Diphosphate
  • Phosphate ion
  • Energy
90
Q

Why is ATP not a good long term energy store ?

A
  • The bonds between the phosphate groups in ATP are unstable

- Carbs and fats are a lot better for this

91
Q

Why is it unstable ?

A

The three phosphate groups repel each other due to the fact that they are all negatively charged.

92
Q

What are the advantages of ATP ?

A
  • 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
Q

What are the properties of ATP ?

A
  • 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
Q

Why is ATP better than glucose ?

A
  • 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
Q

What is phosphorylation ?

A

Phosphorylation is making ATP by adding a phosphate ion on

96
Q

What type of reaction is this ?

A

Condensation reaction as water is removed in this process

97
Q

What are the three types of phosphorylation ?

A
  • Photophosphorylation
  • Oxidative phosphorylation
  • Substrate-level phosphorylation
98
Q

What is Photophosphorylation ?

A

Occurs in the chlorophyll during photosynthesis

99
Q

What is Oxidative phosphorylation ?

A

Occurs in the mitochondria during the electron transport chain ( part of respiration )

100
Q

What is Substrate-level phosphorylation ?

A

When phosphate groups are transferred from donor molecules to ADP

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