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BB10007 Genetics > ✅Molecular Genetics - Araxi Urrutia > Flashcards

✅Molecular Genetics - Araxi Urrutia Flashcards

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1
Q

What is a UTR?

A

Untranslated Regio

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2
Q

Where are UTRs located?

A

At the 5’ and 3’ ends

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3
Q

What is molecular genetics?

A

How DNA, RNA and proteins work

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4
Q

What is transmission genetics?

A

How differences are inherited

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5
Q

What is quantitative genetics?

A

Analysis of how differences are inherited when many loci contribute

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6
Q

What is population/evolutionary genetics?

A

How the different alleles change in frequency over time

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7
Q

How has maize been manipulated?

A

Underwent extreme reshaping during domestication, down to selective breeding or changing parts of the genetic makeup in a lab

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8
Q

What can modern genetics help us to understand?

A

The molecular mechanisms of many diseases

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9
Q

How do BRCA1 and BRCA2 lead to breast cancer?

A

Usually there is one normal copy adn one mutated, but if the functioning copy is not working, the co-activating factor doesn’t bind and cancer can develop

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10
Q

What is preformationism?

A

The idea that we are preformed in one of our parents and then just grow into a baby within the womb

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11
Q

How was the idea of preformationism developed?

A

After the use of microscopes and discovery of cells in the 1600s

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12
Q

What is ovism?

A

The idea that new organisms are inside the egg

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13
Q

What is spermism?

A

The idea that new organisms are inside the sperm

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14
Q

What is epigenesis?

A

The idea that new organisms come from a shapeless mass

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15
Q

What is an example of epigenesis?

A

Some people believed that dirty laundry could generate rats

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16
Q

What is panspermism?

A

Particles from different areas of the body converge in the sexual organs to produce a new baby

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17
Q

What is spontaneous generation?

A

New organisms can come from nothing

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18
Q

How did the idea of pangenesis come about?

A

In the early Greek times, when the notion of inheritance of acquired characteristics was proposed, eg people who were good at music passing it on to their children

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19
Q

What is germ plasm theory?

A

Germ line tissue in the reproductive organs contains a complete set of genetic information that is transferred to gametes

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20
Q

What is blending inhertitance?

A

Offspring are a blend of parental traits

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21
Q

When were cells first observed?

A

In 1600s by Leeuwenhoek

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22
Q

What was proposed in the 1830s?

A

Schleiden and Schwann proposed that all organisms are made of cells - CELL THEORY

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23
Q

What was proposed in the 1860s?

A

Pasteur proved that many diseases were caused by bacterial infections, ending the dispute on spontaneous generation

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24
Q

What happened in 1944?

A

Oswald Avery discovered that DNA is the heritable molecule

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25
Q

What happened in 1952?

A

Hershey and Chase confirm that DNA is genetic material

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26
Q

What is a haplotype?

A

A particular set of polymorphisms in a chromosome

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27
Q

Which gene is found in all bacterial transposable elements?

A

A transposase gene

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28
Q

What does heteroplasmy refer to?

A

Cells with a variable mixture of normal and abnormal organelles

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29
Q

What are DNA insulator sequences?

A

Regions which block the action of enhancers when the insulator sequence lies between the enhancer and promoter of the gene

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30
Q

What protein do bacteria have that helps to condense DNA?

A

FtsZ

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31
Q

Why would a smaller genome have evolutionary benefit?

A

Cell division is faster that way

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32
Q

How many chromosomes do bacteria have?

A

One, that is circular

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33
Q

How many replications sites do bacteria have?

A

One, an ORI site

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34
Q

What are plasmids?

A

Small circular DNA molecules with few genes, often in addition to a single circular chromosome

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35
Q

How can plasmids be transferred?

A

Between bacteria of the same species or between species

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36
Q

How large are plasmids?

A

Several thousand to hundreds of thousands of nucleotides long

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37
Q

How many different plasmids does E. coli have?

A

Around 270

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38
Q

What do plasmid genes do?

A

Help in adapting to changing environments, non essential

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39
Q

Where do the DNA strands of a plasmid separate in replication?

A

The oriV site

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40
Q

What are bacterial genes arranged into?

A

Operons

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41
Q

What is an operon?

A

A single transcriptional unit that includes a series of structural genes, a promoter and an operator

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42
Q

What are RNA polymerases attracted to DNA molecules by?

A

Transcription factors

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43
Q

What does RNA polymerase do to DNA?

A

Changes the conformation and starts transcription

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44
Q

Which end can polymerases add nucleosides to?

A

3’

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45
Q

How does E. coli obtain nutrients?

A

From organic molecules, primarily glucose from the gut

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46
Q

What else can E coli process?

A

Lactose

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47
Q

What enzyme is used by E coli to break down lactose?

A

Beta galactosidase

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48
Q

How does lactose enter the bacteria cell?

A

Via active transport

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49
Q

Which protein is used to actively transport lactose?

A

Permease

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50
Q

What is the lactose broken down into?

A

Glucose and galactose

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51
Q

What else can the lactose be converted into?

A

Allolactose

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52
Q

What is the function of allolactose?

A

It can regulate lactose metabolism

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53
Q

What other enzyme is produced by the lac operon?

A

Thiogalactosidase transacetylase

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54
Q

What type of operon is the lac operon?

A

A negative inducible operon

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55
Q

What does the lac operon do?

A

Controls the transcription of three genes needed in lactose metabolism

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56
Q

What is lacZ?

A

Beta galactosidase

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57
Q

What is lacY?

A

Permease

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58
Q

What is lacA?

A

Thiogalactosidase transacetylase

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59
Q

What is an example of co-ordinate induction?

A

When lactose is added to a medium the synthesis of the three lac proteins increases 1000 fold

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60
Q

What is upstream of the promoter, lacP?

A

A regulator gene,lacI

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61
Q

What is the lacI gene translated into?

A

A repressor

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62
Q

What is the lacI repressor made up of?

A

4 polypeptides, with binding sites for allolactose and DNA

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63
Q

What does the repressor bind to in the absence of lactose?

A

The lac operator site, blocking RNA polymerase

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64
Q

What happens to the repressor in the presence of lactose?

A

Some is converted to allolactose and the repressor is released from the operator

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65
Q

Why is transcription of the lac operon never completely shut down?

A

Because permease is required to allow lactose into the cell and beta-galactosidase is needed for allolactose production

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66
Q

How does the lac operon gene cluster function?

A

In an integrated fashion to provide rapid response to the presence of absence of lactose

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67
Q

Where are regulatory regions usually located?

A

Upstream of the gene cluster that they control, cis acting

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68
Q

What are the molecules that bind to cis acting sites called?

A

Trans-acting elements

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69
Q

What are inducible operons?

A

Transcription is usually off and needs to be turned on

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70
Q

What is an inducer?

A

A small molecule that turns on transcription

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71
Q

What is a repressible operon?

A

Transcription is usually on and needs to be turned off

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72
Q

What is a co-repressor?

A

A small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription

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73
Q

What is a negative repressible operon?

A

Transcription is blocked when co-repressor binds to regulator allowing it to bind to DNA and block transcription

74
Q

What is a positive repressible operon?

A

Regulatory protein is an activator, transcription is blocked when co-repressor binds to regulator

75
Q

What is a negative inducible operon?

A

Transcription usually occurs when inducer binds to repressor

76
Q

What is a positive inducible operon?

A

Regulatory protein is an activator, transcription occurs when inducer activates regulator

77
Q

What is antisense RNA?

A

Complementary to targeted partial sequence of mRNA, bind to them and can regulate translation

78
Q

What is an example of antisense RNA?

A

ompF in E Coli

79
Q

What does ompF do?

A

It is only translated into protein when extracellular osmolatiry is low

80
Q

What are riboswitches?

A

Regulatory sequences of mRNA molecules where molecules can bind and affect gene expression by influencing the formation of secondary structure in the mRNA

81
Q

How can riboswitches prevent translation?

A

The ribosome binding site is hidden

82
Q

What are rybozymes?

A

Sequences of RNA that can catalyse a variety of biochemical functions.

83
Q

What are transcription profiles?

A

Show the genes turned on/off, similarities between species

84
Q

Who is Professor Douglas Melton?

A

A Harvard researcher who successfully created insulin producing beta pancreatic cells

85
Q

What are the features of eukaryotic genes?

A

Linear chromosomes, condensed chromatin, histones, multiple origins, single gene transcription

86
Q

What is the exception to eukaryotic gene structure?

A

C. Elegans, which has operon like structures

87
Q

What are some similarities between prokaryotic and eukaryotic gene expression?

A

RNA polymerases allow transcription, mRNA transcript is translated into protein by ribosomes, genetic code universal

88
Q

How do promoters work in eukaryotic genomes?

A

Each gene has its own promoter

89
Q

Why are transcription and translation separate processes in eukaryotes?

A

Due to the presence of a nuclear membrane, allows more refined regulation

90
Q

Why are eukaryotes more complex?

A

Their gene expression is much more refined and a more complex process, more fine tuning of genes

91
Q

How many types of RNA polymerase do eukaryotes have?

A

3

92
Q

What does Polymerase I transcribe?

A

rRNAs

93
Q

What does polymerase II transcribe?

A

pre mRNAs, snoRNA, miRNA, snRNA - RNAs that regulate splicing

94
Q

What does polymerase III transcribe?

A

tRNAs, smallRNAs, miRNAs, snRNAs

95
Q

How many types of RNA polymerase do bacteria have?

A

1

96
Q

Why must DNA unwind from histones before transcription?

A

To expose promoter regions

97
Q

What are some of the levels of regulation in eukaryotes?

A

Chromatin remodelling, splicing, processing, degradation, translational regulation, protein modification etc

98
Q

How is chromatin structure regulated?

A

Through epigenetics and chromatin remodelling

99
Q

What is a core promoter?

A

The region where the basal transcription apparatus bind, including TATA box

100
Q

What is the proximal control region/regulatory promoter?

A

Located upstream of the core promoter and where some activators can bind

101
Q

What is an enhancer?

A

DNA sequence stimulating transcription from a distance away from the promoter

102
Q

What are silencers?

A

Elements where transcriptional repressors bind

103
Q

What are some post translational modifications?

A

Splicing, cap and polyA tail

104
Q

What are basal transcription factors?

A

In response to injunctions from activators, they position RNA polymerase at the stat of transcription and initiate the process

105
Q

What do transcriptional activators do?

A

Bind to sites on DNA and stimulate transcription, by stimulating or stabilising the assembly of the basal transcription apparatus

106
Q

What is transcriptional synergy?

A

Increasing the number of activator protein binding sites can increase the efficiency of recruiting the transcription machinery, increasing transcription

107
Q

What does transcriptional stalling allow?

A

Faster transcription of genes when needed, to regulate gene expression of heat-shock proteins and other genes

108
Q

What is chromatin remodelling?

A

Changes in the chromatin structure by re-positioning nucleosomes

109
Q

What does chromatin remodelling allow?

A

Transcription factors to bind to DNA and initiate transcription

110
Q

What is chromatin remodelling mediated by?

A

Complexes binding to specific DNA sites, including transcription factors and regulatory proteins

111
Q

How can chromatin remodelling affect gene expression?

A

Nucleosomes slide along DNA, allowing DNA to be ore accessible to proteins affecting expression, and so that the DNA is in a ore exposed position on the nucleosomes

112
Q

Where does post translational modification occur?

A

In eukaryotes, but not in prokaryotes

113
Q

What does RNA degradation include?

A

5’ cap removal, shortening of poly A tail, degradation of 5’ UTR, coding sequence and 3’ UTR

114
Q

What happens if the 5’ cap removed?

A

It is targeted by machinery to degrade RNA, and not translated

115
Q

What happens if the poly A is removed?

A

The sequence is made unstable and when it arrives at the ribosome it is not translated

116
Q

Why are 3’ Poly A tails important?

A

Because proteins can bind to them and then interact with cap binding proteins to enhance the binding of the ribosome at the 5’ end of the mRNA

117
Q

How can alternative splicing produce a non-functional protein?

A

By placing an early stop codon and producing a truncated protein

118
Q

How were introns discovered?

A

When parts of RNA sequence did not align with the same DNA sequence

119
Q

What is colinearity?

A

Strict correspondence between the RNA molecule transcribed and the protein produced

120
Q

What can colinearity indicate?

A

Deletions or insertions

121
Q

Where were introns first discovered?

A

Adenovirus

122
Q

How were introns/RNA splicing discovered?

A

Single stranded DNA was mixed with RNA and the complementary sequences pair, the DNA reannealed or paired with RNA, wile non-coding regions of DNA formed loops

123
Q

What is alternative splicing?

A

When an intron is excised, sometimes exons are excised with it and once gene can form up to 20 variants

124
Q

Why is alternative splicing important?

A

Because it allows a single gene to produce several protein products

125
Q

What is an example of alternative splicing?

A

The tra gene in flies, males have upstream 3’ splice sites, whereas females spliced to second site, termination codon spliced out with the intron

126
Q

What type of tra do male flies have?

A

Non functional tra protein, triggers development of male characteristics

127
Q

What type of tra do female flies have?

A

Longer transcript not including stop codon, functional tra protein and produces female characteristics

128
Q

What is RNA interference?

A

A regulatory mechanism for translation

129
Q

How are siRNAs and miRNAs produced?

A

When RNA molecules fold to produce double stranded RNA, which is then cleaved by the enzyme dicer to form smaller fragments

130
Q

How large are siRNAs/miRNAs?

A

22 base pairs

131
Q

What can siRNAs and miRNAs do?

A

Inhibit translation by binding with/degrading mRNA

132
Q

How do miRNAs inhibit translation?

A

One strand combines with proteins to from silencing complex, prevents translation

133
Q

How do siRNAs inhibit translation?

A

One strand combines with the mRNA and leads to degradation

134
Q

What can some microRNAs do?

A

Methylate histones or DNA by attaching to sequences and attracting methylation enzymes

135
Q

What is VEGF-A?

A

Vascular Enthothelial Growth Factor

136
Q

What does VEGF-A do?

A

Protein which promotes development of new blood vessels, normally after injury to restore blood supply, but also in cancer tumours where increased expression improves blood supply

137
Q

Why are mitochondira only inherited from the mother?

A

Forces reduction at every generation in diversity

138
Q

What has happened to some species that have lost chloroplasts?

A

Some mitochondrial genes are still present in their genomes

139
Q

What can mitochondria and chloroplasts exchange genetic material with?

A

The nucleus

140
Q

Why have some mitochondrial genes migrated to the nucleus?

A

So that the nucleus can have full control over the mitochondria, dependent on protein synthesis

141
Q

What are mitochondira dependent on?

A

Nuclear transcription

142
Q

What do chloroplasts contain?

A

Circular, double stranded DNA

143
Q

How many base pairs do chloroplast genomes have?

A

80,000 - 600,000

144
Q

How are chloroplast genomes arranged?

A

In operons, as in bacteria

145
Q

What type of DNA do chloroplast genomes contain large amounts of?

A

Non-coding

146
Q

What are chloroplasts similar to?

A

Eubacteria

147
Q

What are chloroplasts used for?

A

Assessing phylogenetic relationships

148
Q

What size are mitochondrial genomes?

A

6000 bp to several million

149
Q

What is the mitochondrial genome associated with?

A

Proteins similar to histones

150
Q

Where are most mitochondrial proteins encoded for?

A

The nucleus

151
Q

How do human mitochondrial genomes compare to other species

A

Quite small

152
Q

What produces free radicals?

A

Cellular respiration

153
Q

How can free radicals affect DNA?

A

They damage ir

154
Q

What is heteroplasmy?

A

Multiple distinct DNA sequences within the cytoplasm of a single cell

155
Q

What is homoplasmy?

A

Copies of mitochondiral DNA are all identical

156
Q

What is a contig?

A

A set of overlapping fragments that form a continuous stretch of DNA

157
Q

Where did the idea to sequence the human genome come from?

A

In the 1980s, many genes had been linked to a variety of physiological processes and diseases

158
Q

What was the aim of the Human Genome Project?

A

To obtain the entire DNA sequence of the haploid human genome

159
Q

What were the features of the International Human Genome Sequence Consortium?

A

Headed by Francis Collins, with public funding, free access and started earlier than other projects

160
Q

What method did the IHGSC use?

A

Mapping overlapping clones method

161
Q

What were the features of the Celera project?

A

Headed by Craig Venter, private funding

162
Q

What method did Celera use?

A

Whole genome shotgun technique

163
Q

What was done in the IHGSC strategy?

A

Human genome partitioned into large sequences and stored in yeast mini chromosomes, then each one sequences and assembled using a genetic map

164
Q

What was done in the Celera strategy?

A

Small insert clones were prepared directly from genomic DNA and sequenced in a highly automated way

165
Q

Which effort was deemed to be more successful?

A

Celera, it was cheaper and faster and the shotgun method was used to finish the human genome project

166
Q

What is genomics?

A

The study of genomes using a variety of tools

167
Q

What is structural genomics?

A

Determines the DNA sequences of entire genomes, aims to understand the organisation and sequences of genetic information contained within a genome

168
Q

How many genes are in the human genome?

A

Around 20,000

169
Q

What are transposons?

A

‘Jumping genes’, DNA sequences which can change their position in a genome

170
Q

Approximately how much of the genome codes for proteins?

A

1.5%

171
Q

What is comparative genomics?

A

Refers to the comparison of genomes to understand evolution of genes and species and the function of genes

172
Q

What are homologs?

A

Genes that are evolutionarily related

173
Q

What are orthologs?

A

Homologous genes in different species that evolved from the same gene in a common ancestor

174
Q

What are paralogs?

A

Homologous genes arising by duplication of a single gene in the same organism

175
Q

What is the difference between orthologs and paralogs?

A

Orthologs are in the same organism, paralogs are in different organisms

176
Q

How can the importance of a gene be determined by its rate of evolution?

A

Genes which show accelerated evolution tend to have greater influence

177
Q

What is fundamental genomics?

A

Determines the functions of genes using genomic based approaches

178
Q

What is the transcriptome?

A

All the RNA molecules transcribed from a genome

179
Q

What is transcriptomics?

A

Assessment of gene activity of many genes at a time

180
Q

What are microarrays?

A

Nucleic acid hybridisation, using a known DNA fragment as a probe to find a complementary sequence

181
Q

What is next generation sequencing?

A

Sequencing RNA fragments which are then annotated by aligning them to a reference genome sequence

BB10007 Genetics (3 decks)

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