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Molecular Biology and Genetics > Book 1: Human molecular genetics > Flashcards

Book 1: Human molecular genetics Flashcards

1
Q

How many macromolecules exist in molecule genetics?

A

3.

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2
Q

Which are the 3 macromolecules that define molecular genetics?

A
  1. Proteins.
  2. DNA.
  3. RNA.
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3
Q

What is DNA in organisms?

A

The genetic material.

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4
Q

What is the function of DNA?

A

Transmitted to daughter cells when cells replicate.

Transmitted from generation to generation when organisms reproduce.

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5
Q

What do viruses have?

A

Genetic material.

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6
Q

Where is virus’ genetic material transmitted?

A

To viral progeny.

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7
Q

What are the types of virus’ genetic material?

A

DNA.

RNA.

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8
Q

On what does the type of virus’ material depend?

A

On the virus’ type.

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9
Q

What is the genome of an organism?

A

Different DNA molecules set.

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10
Q

What do all the proteins have?

A

A polypeptide core.

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11
Q

How is the polypeptide core of proteins synthesized?

A

By using genetic information in DNA molecules.

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12
Q

How is the genetic information stored in cells?

A

In DNA molecules.

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13
Q

Why are genetic information stored in DNA and not in RNA anymore?

A

DNA is more chemically stable.
It can be copied accurately.
Transmitted to daughter cells and to generations.

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14
Q

Where are DNA molecules found in eukaryotes?

A

In the chromosomes of nucleus.

Mitochondria.

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15
Q

Where is the DNA stored in plants?

A

In chloroplasts.

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16
Q

What are genes?

A

Segments of hereditary DNA/RNA molecules.

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17
Q

What do genes make?

A

A polypeptide.

A mature functional RNA.

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18
Q

What do polypeptides and RNA molecules make?

A

Working molecules.

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19
Q

With what molecules are polypeptides complexed?

A

Carbohydrates.
Lipids.
Other polypeptides.

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20
Q

How is the DNA packed in simple organisms?

A

With genes.

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21
Q

How are genes packed in more complex eukaryotic cells?

A

Distributed within DNA.

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22
Q

Of what does DNA consist in multicellular eukaryotes?

A

Of repetitive sequences.

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23
Q

How is a coding RNA sequence called?

A

Messenger RNA (mRNA).

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24
Q

What is the function of mRNA?

A

Carries information from DNA to protein synthesis.

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25
Q

Where is mRNA made?

A

In nucleus.

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26
Q

Where is mRNA exported?

A

In cytoplasm.

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27
Q

Why is MRNA exported in cytoplasm?

A

To make proteins.

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28
Q

Where else can mRNA synthesise proteins?

A

In mitochondria.

Chloroplasts.

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29
Q

What is the characteristic of noncoding RNA sequences?

A

Second class of RNA.
Not used as template to make polypeptides.
Act in general way.
Regulate small genes’ expression.

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30
Q

What do proteins represent?

A

The major DNA endpoint information.

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31
Q

How does genetic information generally flow?

A

In a one-way direction.

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32
Q

Why is DNA encoded?

A

To make RNA.

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33
Q

Why is RNA coded?

A

To make polypeptides.

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34
Q

What do polypeptides form?

A

Proteins.

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35
Q

Why the flow of genetic information has been described as the central dogma of molecular biology?

A

Because of its universality.

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36
Q

How many sequential processes are essential in all cellular organisms?

A

2.

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37
Q

Which are the 2 processes essential in organisms?

A
  1. Transcription.

2. Translation.

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38
Q

What happens in transcription?

A

A sequence of bases on a DNA strand is used as a template –> RNA polymerase –> synthesises RNA.

RNA product –> makes mRNA.

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39
Q

What happens in translation?

A

mRNA is decoded –> makes polypeptides at ribosomes.

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40
Q

Where are large RNA-protein complexes found?

A

In cytoplasm.
In mitochondria.
In chloroplasts.

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41
Q

Where is genetic information encoded?

A

In linear sequence of nucleotides in DNA.

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42
Q

When is genetic information copied?

A

During transcription.

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43
Q

Why is genetic information copied during transcription?

A

To specify a linear sequence of nucleotides in RNA product.

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44
Q

What is read in a linear sequence to specify amino acids’ sequence in polypeptide product?

A

3 nucleotides at a time = codons.

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45
Q

What do RNA viruses have?

A

An RNA genome.

A gene that makes reverse transcriptase.

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46
Q

What happens in a reverse transcriptase of RNA viruses?

A

DNA polymerase uses RNA template –> make DNA sequence copy.

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47
Q

What do many DNA sequences in our cells specify?

A

Reverse transcriptase.

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48
Q

Why do many DNA sequences in our cells have reverse transcriptase?

A

To allow DNA copies to be made from different RNAs.

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49
Q

Where is the reverse flow of genetic information from RNA to DNA important?

A

In the evolution of our genome.

Replication of DNA sequences at end of linear chromosomes.

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50
Q

What do all proteins have?

A

A linear polypeptide backbone with carbohydrate, lipid, and small chemical groups added.

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51
Q

What are DNA and RNA strands?

A

Large polymers.

With very similar structures.

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52
Q

What does each of DNA and RNA strands have?

A

A linear sugar-phosphate backbone.
Alternating parts of a five-carbon sugar and a phosphate.
A nitrogenous base attached to each sugar part.

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53
Q

What are the sugars in RNA and DNA?

A

RNA sugar: ribose.

DNA sugar: deoxyribose.

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54
Q

What is the difference between DNA and RNA sugars?

A

Lack (DNA)/possessing (RNA) -OH group at 2’-carbon positions.

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55
Q

What does identify the nucleic acid and determine its function?

A

Sequence of bases.

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56
Q

Of what do the bases of a nucleic acid consist?

A

Heterocyclic rings: carbon + nitrogen atoms.

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57
Q

What are the 2 structural classes bases are divided into?

A
  1. Purines.

2. Pyrimidines.

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58
Q

What do purines have?

A

2 interlocked rings.

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59
Q

What do pyrimidines have?

A

A single ring.

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60
Q

What are there in both DNA and RNA?

A

4 principal base types.
2 purines.
2 pyrimidines.

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61
Q

Which are the common bases in both DNA and RNA?

A

Adenine.
Cytosine.
Guanine.

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62
Q

Which is the fourth in each of DNA and RNA?

A

DNA: Thymine.
RNA: Uracil.

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63
Q

What is the difference between thymine and uracil?

A

Uracil lacks 5-methyl group found in thymine.

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64
Q

To what is each base attached in nucleic acids?

A

To sugar.

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65
Q

How is each base attached to a sugar in nucleosides?

A

By an N-glycosidic bond.

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66
Q

What does N-glycosidic bond join in nucleosides?

A

A nitrogen to carbon 1’ of sugar.

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67
Q

What is a nucleoside?

A

Sugar attached to a base.

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68
Q

What is the basic repeat unit of a DNA strand?

A

A nucleoside with a phosphate group attached at 5’ or 3’ carbon of sugar.

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69
Q

How is the nucleoside with a phosphate group attached at 5’ or 3’ carbon of a sugar called?

A

A nucleotide.

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70
Q

What else does DNA contain?

A

Minor base.

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71
Q

By what are minor base types produced?

A

Chemical modification.

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72
Q

By what are proteins composed?

A

One/more polypeptide chains.

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73
Q

How can polypeptide chains be modified?

A

BY addition of carbohydrate side chains.

Other chemical groups.

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74
Q

What are polypeptides?

A

Polymers.

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75
Q

What do polypeptides have?

A

A linear sequence of repeating units.

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76
Q

How are the repeating units of polypeptides called?

A

Amino acids.

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77
Q

What happens to amino acids in their electrically neutral form?

A

Amino group connected by a-carbon atom to carboxyl group.

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78
Q

What does an identifying side chain determine in amino acids?

A

Their chemical nature.

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79
Q

What does the amino group gain at neutral pH?

A

A proton.

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80
Q

How does the amino group become once it gains a proton at neutral pH?

A

Positively charged.

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81
Q

What does the carboxyl group of amino acids lose at neutral pH?

A

A proton.

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82
Q

How does the carboxyl group of amino acids become once it loses a proton at neutral pH?

A

Negatively charged.

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83
Q

What does a polypeptide have?

A

A repeating backbone.

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84
Q

What happen on the repeating backbone of polypeptides?

A

Amino acids linked by amide groups by peptide bonds.

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85
Q

Into how many groups can the 20 different amino acids be classified?

A

3 main groups.

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86
Q

What do covalent bonds require to break?

A

High energy input.

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87
Q

How can noncovalent bonds break?

A

At physiological temperatures.

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88
Q

When are hydrogen bonds formed?

A

When H+ interacts with electron atoms: O2/Ni.

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89
Q

Where do ionic interactions occur?

A

Between charged groups.

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90
Q

Where are ionic interactions weak and when strong?

A 
Weak = in aqueous environments.
Strong = in crystals.
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91
Q

Where are ionic bonds important?

A

In biological function.

Enzyme-substrate recognition.

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92
Q

What do Van der Waals forces show?

A

Weak attractive bonding interaction.

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93
Q

Why do Van der Walls force have weak bonding?

A

Due to electrical charges.

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94
Q

What happens when atoms become extremely close?

A

Knockout each other strongly.

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95
Q

Where can Van der Walls forces be important?

A

Between surfaces of 2 macromolecules.

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96
Q

What is the cellular environment?

A

Aqueous.

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97
Q

What is the structure of water?

A

Complex.

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98
Q

What does the water structure include?

A

Rapid network.

Noncovalent bonding.

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99
Q

What is the most important force in water molecules?

A

Hydrogen bond.

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100
Q

What is hydrogen bond?

A

Weak.

Electrostatic.

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101
Q

Where does hydrogen bond occur?

A

Between positive hydrogen atoms and negative atoms.

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102
Q

What is a characteristic of charged molecules?

A

highly soluble in water.

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103
Q

What are DNA and RNA based on the phosphate groups of their nucleotides?

A

Negatively-charged polyanions.

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104
Q

What can proteins be based on their amino acid composition?

A

Neutral.
Positive.
Negative.

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105
Q

When are neutral proteins soluble?

A

If they contain charged/neutral polar amino acids.

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106
Q

Wat are the membrane-bound proteins with many hydrophobic amino acids, in a hydrophobic encironment?

A

Thermodynamically more stable.

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107
Q

What do noncovalent bonds allow?

A

Interactions between different molecules.

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108
Q

Why is hydrogen bonding important?

A

It allows interactions between different nucleic acids.

Facilitates recognition by regulatory RNAs of target sequences in other rRNAs/DNA.

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109
Q

How are neighbouring sugars linked?

A

By 3’- 5’ phosphodiester bonds.

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110
Q

What happens in 3’- 5’phosphodiester bonds?

A

Phosphate group links 3’ carbon of one sugar to 5’ carbon of next sugar-phosphate backbone.

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111
Q

What is the genetic material of viruses?

A

Single-stranded DNA.

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112
Q

How many species does each cellular DNA species have?

A

2 DNA strands.

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113
Q

How are the 2 DNA strands structured?

A

As a double helix.

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114
Q

What happens in the double helix?

A

Strands curve around each other.

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115
Q

How is base pair structured?

A

Each base on one DNA = non-covalently linked to opposed base on opposite DNA strand.

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116
Q

What does base pairing involve?

A

Certain purine-pyrimidine combinations only.

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117
Q

When doe the 2 DNA strands fit together correctly in double- stranded DNA?

A

When opposite every A on one strand is a T on the other strand and when opposite every G is a C.

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118
Q

Which base pairs are accepted in DNA?

A

A-T.

G-C.

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119
Q

By how many hydrogen bonds are base pairs held together in the Watson-Crick model of DNA?

A

G-C: 3 bonds.

A-T: 2 bonds.

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120
Q

Which bonds are stronger in the DNA molecule?

A

The 3 hydrogen bonds between G-C pairs.

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121
Q

How is the base composition of DNA measured?

A

Amount of A% = amount of T%.
Amount of G% = amount of C%.

Total = 100%.

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122
Q

What does a nucleic acid strand have?

A

Asymmetric ends.
5’ end C not linked to another sugar.
3’ end C not involved in phosphodiester bonding.

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123
Q

What is the orientation of each nucleic acid strand?

A

5’ –> 3’.

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124
Q

In what orientation must 2 strands which form a duplex be?

A

In an antiparallel arrangement.

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125
Q

What do we mean by ‘antiparallel arrangement of duplex DNA’?

A

5’ –> 3’ direction of one DNA strand = opposite to its partner’s orientation.

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126
Q

Why are the hydrogen bonds formed in base pairing important?

A

They form a double helix.

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127
Q

Why are the base-stacking forces important?

A

They stabilise the helix between adjacent bases.

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128
Q

What are the characteristics of double helix?

A

Rigid.

Uniform structure

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129
Q

What can double helix undergo?

A

Local changes.

Alternative base pairing types.

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130
Q

Which base pairs can make the minor groove of double helix narrower?

A

A-T base pairs.

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131
Q

What is an alternative type of double helix that can be formed?

A

Z-type DNA double helix.

132
Q

What can the base pairs in DNA adopt?

A

Different geometries.

133
Q

What is an example of different geometry of base pairs in DNA?T

A

Flipped base pairing –> rotation of bases close to 180 degrees around N-glycosidic bond –> forms Hoogsteen base pairs.

134
Q

What are the telomeres?

A

The specialised sequences at the ends of linear chromosomes.

135
Q

What are the cytokine modifications?

A

Epigenetic marks important for regulating gene expression.

136
Q

For how much distance do bases show perfect matching in a double-stranded DNA in humans?

A

Over 249 million nucleotides.

137
Q

What do the 2 DNA strands of a duplex exhibit?

A

Base complementarity.

138
Q

What do the 2 DNA strands of a duplex have?

A

Complementary base sequences.

139
Q

By what is the genetic information encoded?

A

By the linear sequence of bases in DNA strands.

140
Q

How are nucleic acids defined?

A

By their base sequences.

141
Q

In which direction are base sequences written?

A

In the 5’–>3’ direction.

142
Q

What is the 5’ –> 3’ direction about?

A

The direction of synthesis of new DNA/RNA from a DNA template.

143
Q

How must the sequence of a single-stranded oligonucleotide be written?

A

Accurately: 5’ p-C-p-G-p-A-p-C-p-C-p-A-p-T-OH 3’.

144
Q

How can we make a complementary DNA strand: 3’ –> 5’?

A

By the template strand (given): 5’ –> 3’.

145
Q

How is DNA replication characterised?

A

Semi-conservative.

146
Q

What must happen to each double-stranded DNA before cell divide?

A

They must be replicated.

147
Q

Why must each double-stranded DNA be replicated before cells divide?

A

To generate 2 identifiable double helices, 2 daughter cells.

148
Q

What must happen first in DNA replication?

A

The 2 DNA strands of original double helix –> unwound.

149
Q

How can the 2 DNA strands be unwound?

A

By a DNA helicase.

150
Q

What happens to the 2 unwound DNA strands?

A

Each is used as a template by a DNA polymerase.

151
Q

What does each template strand make?

A

A complementary DNA strand.

152
Q

How are the complementary strands made?

A

With 4 deoxy nucleoside triphosphates: dNTPS.

153
Q

What is dNTPS?

A

A combination of dATP, dCTP, dGTP, and dTTP.

154
Q

What does the DNA Polymerase do?

A

Cleaves the dNTP precursors between first and second phosphates.

155
Q

How is DNA synthesis initiated?

A

By using an RNA primer and a specialised primase enzyme.

156
Q

What happens in DNA synthesis?

A

The new DNA chain grows.

157
Q

How does the new DNA chain grow?

A

By adding nucleotides one at a time to the 3’.

158
Q

How are nucleotides added to make the new DNA strand?

A

By using a DNA-dependent DNA polymerase and dNTPS.

159
Q

How is the DNA synthesis reaction driven?

A

By the change in free energy when dNTP is cleaved at phosphoanhydrite bond between first and second phosphate.

160
Q

Of what does the parental duplex consist?

A

Of 2 complimentary DNA strands.

161
Q

What does each completed daughter DNA duplex contain?

A

One of the 2 parental DNA strands + one newly synthesized DNA strand.

162
Q

To what is each completed daughter DNA duplex identical?

A

To each other and to the original parental DNA duplex.

163
Q

How is DNA replication characterised due to the fact that each daughter duplex has one strand from the original DNA and one new DNA strand?

A

Semi-conservative.

164
Q

How are the specific points, DNA replication is initiated called?

A

Origins of replication.

165
Q

What is the overall direction of chain growth for one newly synthesized daughter strand?

A

5’–>3’.

166
Q

What is the direction for the lagging strand?

A

3’ –> 5’.

167
Q

What do the reactions catalysed by DNA polymerase involve?

A

Adding dNMP residues to the free 3’ hydroxyl group of the growing DNA strand.

168
Q

What does the leading strand always have?

A

A free 3’ hydroxyl group that allows continuous elongation in the same direction as the replication moves.

169
Q

Why is a DNA helicase needed?

A

To open up a replication fork.

170
Q

What does DNA helicase allow?

A

Synthesis of new daughter DNA strands to begin.

171
Q

Why is replication discontinuous?

A

Because lagging strand is synthesized in the opposite direction and is built up in pieces, Okazaki fragments.

172
Q

What happens to the Okazaki fragments?

A

They will be stitched together with a DNA ligase.

173
Q

What does the initiation of the leading strand and of each Okazaki fragments of the lagging strand require?

A

A short RNA primer synthesized and base-paired with the original DNA strand.

174
Q

What will happen to the RNA primers after replication?

A

Will be removed and replaced by a DNA sequence.

175
Q

What is the direction of synthesis of the lagging strand?

A

Opposite to replication fork direction.

176
Q

What is the difference between RNA polymerases and DNA polymerases?

A

DNA polymerases need a primer with a free 3’ hydroxyl end to initiate synthesis.

177
Q

How many RNA primers are needed when synthesizing the leading strand?

A

Just one.

178
Q

What happens due to the fact that synthesis of the lagging strand is discontinuous?

A

An RNA primer is needed to initiate the synthesis of each Okazaki fragment.

179
Q

Where does the machinery for DNA replication rely?

A

On a variety of proteins and RNA primers.

180
Q

How many DNA polymerases do mammalian cells have?

A

20.

181
Q

What do DNA polymerases in our cells use?

A

An individual DNA strand as a template for synthesizing a complementary DNA strand.

182
Q

What do RNA-directed DNA polymerases use in our cells?

A

RNA templates to make complementary DNA sequences.

183
Q

How are RNA-directed DNA polymerases called?

A

Reverse transcriptases.

184
Q

What do DNA-directed DNA polymerases include?

A

DNA polymerases delta and epsilon to copy accurately DNA sequences.

185
Q

What do DNA polymerases do?

A

Replicate most of the nuclear DNA of our cells.

186
Q

What does polymerase delta synthesize?

A

The lagging strand.

187
Q

What does polymerase epsilon synthesize?

A

The leading strand.

188
Q

What do the delta and epsilon enzymes have?

A

Low error rates.

189
Q

Why do delta and epsilon polymerases have low error rates?

A

Because they have an associated 3’ -5’ exonuclease activity responsible for proofreading.

190
Q

What do the epsilon and delta polymerases do in proofreading?

A

If a mistake is made –> wrong base is inserted at 3’ hydroxyl group of growing DNA chain –> 3’ -5’ exonuclease snips it out –> the correct base is inserted.

191
Q

What does initiation of DNA replication and of Okazaki fragments require?

A

DNA polymerase alpha.

192
Q

What id the DNA polymerase alpha?

A

polymerase complex + primase.

193
Q

What does DNA polymerase alpha lack?

A

Own proofreading function.

194
Q

What happens in polymerase alpha?

A

Errors made in base incorporation are corrected without needing polymerase delta.

195
Q

What does DNA polymerase gama have?

A

An intrinsic proofreading exonuclease activity.

196
Q

What does polymerase gama synthesize?

A

Mitochondrial DNA.

197
Q

Where do DNA polymerases function?

A

Recombination and DNA repair.

198
Q

Which are the major classes of proteins involved in DNA replication?

A
  1. Topoisomerases.
  2. Helicases.
  3. Single-strand-DNA binding proteins.
  4. Primases.
  5. DNA polymerases.
  6. DNA ligases.
199
Q

What do topoisomerases do?

A

Break a single DNA strand –> release tension –> helix uncoiled form –> DNA unwound.

200
Q

What do helicases do?

A

Unwind double helix at replication fork.

201
Q

What do single-strand-DNA binding proteins do?

A

Maintain stability of replication fork.

Protect single-stranded DNA from being degraded.

202
Q

What do primases do?

A

Attach a primer to single-stranded DNA at replication fork.

203
Q

What do DNA polymerases do?

A

Synthesize new DNA strands.

204
Q

What do DNA ligases do?

A

Seal nicks that remain in newly synthesized DNA after RNA primers are removed and small gaps are filled in by DNA polymerase.

Catalyse information of a phosphodiester bond between unattached adjacent 3’ OH and 5’ phosphate groups.

205
Q

What is RNA normally?

A

Single-stranded.

206
Q

What do certain RNA viruses have?

A

A double-stranded RNA genome.

207
Q

How can double-stranded RNA be formed by a single-stranded RNA genome?

A

Transcription of RNA sequences –> make a complementary RNA.

208
Q

What do RNA molecules need to have?

A

RNA-RNA base pairing.

209
Q

What do RNA sequences form when they engage with DNA sequences?

A

RNA-DNA duplexes.

210
Q

When is an A-type double helix formed rather than the common B-type helix?

A

When a 2’ hydroxyl group is present on ribose sugar of an RNA-RNA or an RNA-DNA duplex.

211
Q

What is it important in shaping the structure of a single-stranded RNA?

A

Hydrogen bonding.

212
Q

Where else is hydrogen bonding important in single-stranded RNA?

A

Functional, short, double-stranded sequence recognised by specific RNA-binding proteins.

213
Q

What are the most common type of secondary structure?

A

Hairpin structures.

214
Q

Of what is the genome in many viruses made up?

A

One type of nucleic acid: single-stranded DNA, double-stranded DNA, single-stranded RNA, double-stranded RNA.

215
Q

How can viruses be classified?

A

+ viruses.

- viruses.

216
Q

Where do DNA viruses replicate?

A

In nucleus.

217
Q

Where do RNA viruses replicate?

A

In cytoplasm.

218
Q

What does RNA replication have higher than DNA replication?

A

Error rate.

219
Q

What does the elevated mutation rate allow RNA viruses?

A

Adapt rapidly to changing environmental conditions.

220
Q

What are the retroviruses?

A

RNA viruses.

221
Q

Where do retroviruses replicate?

A

In nucleus.

222
Q

Into what is the single-stranded RNA genome of retroviruses converted?

A

A single-stranded complementary DNA.

223
Q

How is the single-stranded RNA genome of retroviruses converted into a single-stranded complementary DNA?

A

By using a viral reverse transcriptase.

224
Q

What happens to the complementary DNA?

A

Converted into a double-stranded DNA.

225
Q

How is cDNA converted into a double-stranded DNA?

A

By using a DNA polymerase from the host cell.

226
Q

What do viral proteins do?

A

Help instert the double-stranded DNA into the genome of the host cell.

227
Q

What happens to the double-stranded DNA once it enters the genome of the host cell?

A

It remains for long periods or is used to synthesize new viral RNA genomes packaged as new virus particles.

228
Q

Where is DNA replication initiated?

A

At origins of replication.

229
Q

What does DNA replication generate?

A

Y-shaped replication forks.

230
Q

What happens in Y-shaped replication forks?

A

The parental DNA duplex is opened up.

231
Q

What do the antiparallel parental DNA strands do?

A

Serve as templates for the synthesis of complementary daughter strands which run in opposite directions.

232
Q

What is the direction of one newly synthesized daughter, leading strand?

A

5’ –> 3’.

233
Q

What is the direction of the other daughter lagging strand?

A

3’ –> 5’.

234
Q

What do the reactions catalysed by DNA polymerase involve?

A

Adding dNMP residues to the free 3’ hydroxyl group of the growing DNA strand.

235
Q

Which strand has a free 3’ hydroxyl group that allows continuous elongation in the same direction where the replication fork moves?

A

Only the leading strand.

236
Q

What does a DNA helicase do?

A

Opens up a replication fork –> synthesis of new daughter DNA strands begins.

237
Q

How is replication characterised?

A

Semi-discontinuous.

238
Q

Why is replication semi-discontinuous?

A

Lagging strand is synthesized in the opposite direction –> built up in pieces Okazaki fragments A, B, C.

Leading strand is synthesized continuously.

239
Q

How will the Okazaki fragments stich together?

A

Using DNA ligase.

240
Q

What are the Okazaki fragments?

A

100-1000 nucleotides joined by enzyme DNA ligase that make the lagging strand, in opposite direction of replication fork.

241
Q

How is the leading strand synthesized?

A

Continuously.

242
Q

Can DNA polymerases initiate synthesis?

A

No.

243
Q

When can DNA polymerases initiate synthesis?

A

Only when a short oligonucleotide primer with a free 3’ hydroxyl end is provided.

244
Q

For what are RNA primers needed?

A

Initiating synthesis.

245
Q

By what are RNA primers synthesized?

A

DNA primase.

246
Q

How many RNA primers are needed in synthesis?

A

Only one.

247
Q

What happens in synthesis of Okazaki fragments?

A

An RNA primer is needed to initiate synthesis of each fragment.

248
Q

How will the RNA primer be removed?

A

With a 5’ –> 3’ exonuclease.

249
Q

By what will the RNA primers replaced after synthesis?

A

By the corresponding DNA sequence.

250
Q

On what does the machinery for DNA replication rely?

A

On proteins.
On RNA primers.
On evolution.

251
Q

Where is DNA replication more compelx?

A

In eukaryotes.

252
Q

How many DNA polymerases do mammalian cells have?

A

20.

253
Q

What does each DNA polymerase have?

A

Special function.

254
Q

What are most of the DNA polymerases in our cells?

A

DNA-directed.

255
Q

What do DNA polymerases do in our cells?

A

Use an individual DNA strand as a template –> synthesise a complementary DNA strand.

256
Q

What other polymerases do we have in our cells?

A

RNA-directed DNA polymerases.

257
Q

How are RNA-directed DNA polymerases named?

A

Reverse transcriptases.

258
Q

What do RNA-directed DNA polymerases do?

A

Use RNA templates –> make complementary DNA sequences.

259
Q

How many structures does a double helix have?

A

3.

260
Q

What are the 3 structures of the double helixes?

A

A-form.
B-form.
Z-form.

261
Q

What is the difference between the A-form and the B-form?

A

A-form is shorter and wider.

Has a deep, narrow major groove.

262
Q

When does A-DNA structure exist?

A

Only under non-physiological conditions.

263
Q

Where .can G-U base pairing occur?

A

In short regions of double-stranded RNA in the RNA strand.

264
Q

Is the G-U base pairing stable?

A

No.

265
Q

Does the G-U base pairing distort the RNA-RNA helix?

A

No.

266
Q

What can DNA have?

A

Cell-type specific function.

267
Q

Why can DNA have cell-type specific functions?

A

Because it contains sequences used to make RNA and polypeptides which differ from cell to cell.

268
Q

What are genes?

A

Discrete DNA segments.
Spaced at irregular intervals in the DNA strand.
Serve as templates.

269
Q

Why do genes serve as tmplates?

A

To make complementary RNA sequences in transcription.

270
Q

What must the initial primary RNA transcript undergo?

A

Maturation steps.

271
Q

Why must the primary RNA transcript undergo maturation steps?

A

To make the mature functional mRNA.

272
Q

What does the mature mRNA do?

A

Serves as template –> makes a polypeptide.

273
Q

What are the gene products needed for?

A

Vital cell processes = DNA Replication, protein synthesis.

274
Q

When are proteins and RNA products made in specific cell types and not in all?

A

In B and T lymphocytes which make immunoglobulins and T-cell receptors.

275
Q

What are the DNA compositions of the different cell types in an organism?

A

Identical.

276
Q

Why is there variation in cells in an organism?

A

Because there are gene expression differences in transcription.
Different genes are transcribed.

277
Q

On what does gene expression depend?

A

On cells’ needs.

278
Q

What does transcription mean?

A

RNA –> synthesized

Using DNA-directed RNA polymerases.

279
Q

What happens in transcription?

A

DNA strands = templates for RNA synthesis.

280
Q

Where is RNA synthesized in eukaryotic cells?

A

In nucleus.

281
Q

What is transcribed in eukaryotic cells?

A

Nuclear genes.

282
Q

Where is a small amount of genes transcribed.

A

In mitochondria.

Chloroplasts.

283
Q

How are genes transcribed in mitochondria and chloroplasts?

A

DNA in organelles –> transcribed.

284
Q

Where are chloroplasts found?

A

In plant cells.

285
Q

What happens to the DNA during transcription?

A

DNA helix –> unwound locally –> separated DNA strand –> RNA polymerase comes –> makes a complementary RNA sequence.

286
Q

Where is RNA polymerase and DNA polymerase used?

A

RNA Polymerase: Transcription.

DNA Polymerase: DNA Replication.

287
Q

What does the RNA transcript have?

A

A complementary sequence of the template DNA strand.

5’ - 3’ direction.

Base = U instead of T.

Base sequence as the nontemplate DNA strand.

288
Q

How is the nontemplate called?

A

Sense strand.

289
Q

How is the template strand called?

A

Antisense strand.

290
Q

Which DNA strand is used by the RNA polymerase as a template to synthesize a complementary RNA strand?

A

The template strand.

291
Q

From what is the RNA strand synthesized?

A

Ribonucleoside triphosphate precursors. (rNTPs).

292
Q

What does the polymerase do to synthesize RNA?

A

Opens rNTPs –> gives Ribonucleoside monophosphates (rNMPs).

293
Q

How are the rNMPs inserted?

A

One nucleotide as a time.

294
Q

How are the rNMPs inserted?

A

Join the 3’OH of previous nucleotide based on base pairing rules.

295
Q

On what is RNA transcription based?

A

Base Pairing rules.

296
Q

On which DNA strand will the RNA strand be complementary and on which identical?

A

Complementary to the template strand.

Identical to the sense strand.

297
Q

From which 4 precursors does RNA Polymerase synthesize RNA?

A

ATP, CTP, GTP, UTP.

298
Q

What does elongation involve?

A

Addition of appropriate ribonucleotide monophosphate: AMP, CMP, GMP, UMP to 3’OH end of growing RNA strand.

299
Q

How can transcription run ffectively?

A

Various proteins bind DNA sequence –> guide RNA Polymerase.

300
Q

What is also important to be added in transcription?

A

DNA elements.

301
Q

How many classes of DNA-dependent RNA polymerase occur in eukaryotic cells?

A

4.

302
Q

Where are the 3 DNA-dependent RNA polymerase classes used?

A

Transcribing nuclear genes.

303
Q

Where is the last DNA-dependent RNA polymerase used?

A

Transcribing mitochondiral DNA.

304
Q

By what is the mitochondrial RNA polymerase encoded?

A

Nuclear gene.

305
Q

How is the mitochondrial DNA transcribed?

A

Nuclear gene –> encoded –> mRNA –> cytoplasm –> ribosomes –> translation –> mitochondria.

306
Q

What is the difference between DNA Polymerases and RNA polymerases?

A

RNA polymerases do not need primer to initiate RNA synthesis.

307
Q

What do RNA polymerases need to start transcription process?

A

Protein regulators = transcription factors .

308
Q

What do transcription factors do?

A

Bind to certain DNA sequences with gene –> activate transcription process.

309
Q

To what can a transcription factor bind?

A

To a promoter.

310
Q

What is a promoter?

A

A collection of closely spaced short DNA sequence elements in a gene neighbourhood.

311
Q

What do transcription factors activate once they bind to a promoter?

A

The RNA Polymerase.

312
Q

Where are promoters and primase used?

A

Promoter: RNA Polymerase –> transcription.
Primer: DNA Polymerase –> DNA replication.

313
Q

What are the transcription factors?

A

Trans-acting.

314
Q

Why are the transcription factors trans-acting?

A

Because they are produced be remote genes –> migrate –> to sites of action.

315
Q

What are the promoter sequences?

A

Cis-acting?

316
Q

Why are the promoters cis-acting?

A

Because the are located on the same DNA molecule where they regulate the genes.

317
Q

For what is the RNA polymerase 2 responsible?

A

Transcribing all protein coding genes in nucleus + important genes encoding noncoding RNAs.

318
Q

Where does RNA polymerase 2 rely?

A

Transcription factors.
Tissue specific
Cell specific factors

319
Q

Where does RNA Polymerase 1 occur?

A

Nucleolus.

320
Q

What does RNA Polymerase 1 synthesize?

A

Cytoplasmic ribosomal RNAs.

321
Q

Where does RNA polymerase occur?

A

Nucleoplasm.

322
Q

What does RNA Polymerase 2 synthesize?

A

mRNAs nuclear genes + noncoding RNAs, snRNAs, miRNAs, IncRNAs, snoRNAs.

323
Q

Where does RNA Polymerase 3 occur?

A

Nucleoplasm.

324
Q

What does RNA polymerase 3 synthesize?

A

Small noncoding RNAs, ribosomal RNA, cytosolic tRNAs.

325
Q

Where does RNA Polymerase mt occur?

A

Mitochondria.

326
Q

What does RNA polymerase mt synthesize?

A

RNAs from mitochondrial DNA.

Molecular Biology and Genetics (15 decks)

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