✅Molecular Genetics - Araxi Urrutia Flashcards
1
Q
What is a UTR?
A
Untranslated Regio
2
Q
Where are UTRs located?
A
At the 5’ and 3’ ends
3
Q
What is molecular genetics?
A
How DNA, RNA and proteins work
4
Q
What is transmission genetics?
A
How differences are inherited
5
Q
What is quantitative genetics?
A
Analysis of how differences are inherited when many loci contribute
6
Q
What is population/evolutionary genetics?
A
How the different alleles change in frequency over time
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
8
Q
What can modern genetics help us to understand?
A
The molecular mechanisms of many diseases
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
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
11
Q
How was the idea of preformationism developed?
A
After the use of microscopes and discovery of cells in the 1600s
12
Q
What is ovism?
A
The idea that new organisms are inside the egg
13
Q
What is spermism?
A
The idea that new organisms are inside the sperm
14
Q
What is epigenesis?
A
The idea that new organisms come from a shapeless mass
15
Q
What is an example of epigenesis?
A
Some people believed that dirty laundry could generate rats
16
Q
What is panspermism?
A
Particles from different areas of the body converge in the sexual organs to produce a new baby
17
Q
What is spontaneous generation?
A
New organisms can come from nothing
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
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
20
Q
What is blending inhertitance?
A
Offspring are a blend of parental traits
21
Q
When were cells first observed?
A
In 1600s by Leeuwenhoek
22
Q
What was proposed in the 1830s?
A
Schleiden and Schwann proposed that all organisms are made of cells - CELL THEORY
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
24
Q
What happened in 1944?
A
Oswald Avery discovered that DNA is the heritable molecule
25
What happened in 1952?
Hershey and Chase confirm that DNA is genetic material
26
What is a haplotype?
A particular set of polymorphisms in a chromosome
27
Which gene is found in all bacterial transposable elements?
A transposase gene
28
What does heteroplasmy refer to?
Cells with a variable mixture of normal and abnormal organelles
29
What are DNA insulator sequences?
Regions which block the action of enhancers when the insulator sequence lies between the enhancer and promoter of the gene
30
What protein do bacteria have that helps to condense DNA?
FtsZ
31
Why would a smaller genome have evolutionary benefit?
Cell division is faster that way
32
How many chromosomes do bacteria have?
One, that is circular
33
How many replications sites do bacteria have?
One, an ORI site
34
What are plasmids?
Small circular DNA molecules with few genes, often in addition to a single circular chromosome
35
How can plasmids be transferred?
Between bacteria of the same species or between species
36
How large are plasmids?
Several thousand to hundreds of thousands of nucleotides long
37
How many different plasmids does E. coli have?
Around 270
38
What do plasmid genes do?
Help in adapting to changing environments, non essential
39
Where do the DNA strands of a plasmid separate in replication?
The oriV site
40
What are bacterial genes arranged into?
Operons
41
What is an operon?
A single transcriptional unit that includes a series of structural genes, a promoter and an operator
42
What are RNA polymerases attracted to DNA molecules by?
Transcription factors
43
What does RNA polymerase do to DNA?
Changes the conformation and starts transcription
44
Which end can polymerases add nucleosides to?
3'
45
How does E. coli obtain nutrients?
From organic molecules, primarily glucose from the gut
46
What else can E coli process?
Lactose
47
What enzyme is used by E coli to break down lactose?
Beta galactosidase
48
How does lactose enter the bacteria cell?
Via active transport
49
Which protein is used to actively transport lactose?
Permease
50
What is the lactose broken down into?
Glucose and galactose
51
What else can the lactose be converted into?
Allolactose
52
What is the function of allolactose?
It can regulate lactose metabolism
53
What other enzyme is produced by the lac operon?
Thiogalactosidase transacetylase
54
What type of operon is the lac operon?
A negative inducible operon
55
What does the lac operon do?
Controls the transcription of three genes needed in lactose metabolism
56
What is lacZ?
Beta galactosidase
57
What is lacY?
Permease
58
What is lacA?
Thiogalactosidase transacetylase
59
What is an example of co-ordinate induction?
When lactose is added to a medium the synthesis of the three lac proteins increases 1000 fold
60
What is upstream of the promoter, lacP?
A regulator gene,lacI
61
What is the lacI gene translated into?
A repressor
62
What is the lacI repressor made up of?
4 polypeptides, with binding sites for allolactose and DNA
63
What does the repressor bind to in the absence of lactose?
The lac operator site, blocking RNA polymerase
64
What happens to the repressor in the presence of lactose?
Some is converted to allolactose and the repressor is released from the operator
65
Why is transcription of the lac operon never completely shut down?
Because permease is required to allow lactose into the cell and beta-galactosidase is needed for allolactose production
66
How does the lac operon gene cluster function?
In an integrated fashion to provide rapid response to the presence of absence of lactose
67
Where are regulatory regions usually located?
Upstream of the gene cluster that they control, cis acting
68
What are the molecules that bind to cis acting sites called?
Trans-acting elements
69
What are inducible operons?
Transcription is usually off and needs to be turned on
70
What is an inducer?
A small molecule that turns on transcription
71
What is a repressible operon?
Transcription is usually on and needs to be turned off
72
What is a co-repressor?
A small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription
73
What is a negative repressible operon?
Transcription is blocked when co-repressor binds to regulator allowing it to bind to DNA and block transcription
74
What is a positive repressible operon?
Regulatory protein is an activator, transcription is blocked when co-repressor binds to regulator
75
What is a negative inducible operon?
Transcription usually occurs when inducer binds to repressor
76
What is a positive inducible operon?
Regulatory protein is an activator, transcription occurs when inducer activates regulator
77
What is antisense RNA?
Complementary to targeted partial sequence of mRNA, bind to them and can regulate translation
78
What is an example of antisense RNA?
ompF in E Coli
79
What does ompF do?
It is only translated into protein when extracellular osmolatiry is low
80
What are riboswitches?
Regulatory sequences of mRNA molecules where molecules can bind and affect gene expression by influencing the formation of secondary structure in the mRNA
81
How can riboswitches prevent translation?
The ribosome binding site is hidden
82
What are rybozymes?
Sequences of RNA that can catalyse a variety of biochemical functions.
83
What are transcription profiles?
Show the genes turned on/off, similarities between species
84
Who is Professor Douglas Melton?
A Harvard researcher who successfully created insulin producing beta pancreatic cells
85
What are the features of eukaryotic genes?
Linear chromosomes, condensed chromatin, histones, multiple origins, single gene transcription
86
What is the exception to eukaryotic gene structure?
C. Elegans, which has operon like structures
87
What are some similarities between prokaryotic and eukaryotic gene expression?
RNA polymerases allow transcription, mRNA transcript is translated into protein by ribosomes, genetic code universal
88
How do promoters work in eukaryotic genomes?
Each gene has its own promoter
89
Why are transcription and translation separate processes in eukaryotes?
Due to the presence of a nuclear membrane, allows more refined regulation
90
Why are eukaryotes more complex?
Their gene expression is much more refined and a more complex process, more fine tuning of genes
91
How many types of RNA polymerase do eukaryotes have?
3
92
What does Polymerase I transcribe?
rRNAs
93
What does polymerase II transcribe?
pre mRNAs, snoRNA, miRNA, snRNA - RNAs that regulate splicing
94
What does polymerase III transcribe?
tRNAs, smallRNAs, miRNAs, snRNAs
95
How many types of RNA polymerase do bacteria have?
1
96
Why must DNA unwind from histones before transcription?
To expose promoter regions
97
What are some of the levels of regulation in eukaryotes?
Chromatin remodelling, splicing, processing, degradation, translational regulation, protein modification etc
98
How is chromatin structure regulated?
Through epigenetics and chromatin remodelling
99
What is a core promoter?
The region where the basal transcription apparatus bind, including TATA box
100
What is the proximal control region/regulatory promoter?
Located upstream of the core promoter and where some activators can bind
101
What is an enhancer?
DNA sequence stimulating transcription from a distance away from the promoter
102
What are silencers?
Elements where transcriptional repressors bind
103
What are some post translational modifications?
Splicing, cap and polyA tail
104
What are basal transcription factors?
In response to injunctions from activators, they position RNA polymerase at the stat of transcription and initiate the process
105
What do transcriptional activators do?
Bind to sites on DNA and stimulate transcription, by stimulating or stabilising the assembly of the basal transcription apparatus
106
What is transcriptional synergy?
Increasing the number of activator protein binding sites can increase the efficiency of recruiting the transcription machinery, increasing transcription
107
What does transcriptional stalling allow?
Faster transcription of genes when needed, to regulate gene expression of heat-shock proteins and other genes
108
What is chromatin remodelling?
Changes in the chromatin structure by re-positioning nucleosomes
109
What does chromatin remodelling allow?
Transcription factors to bind to DNA and initiate transcription
110
What is chromatin remodelling mediated by?
Complexes binding to specific DNA sites, including transcription factors and regulatory proteins
111
How can chromatin remodelling affect gene expression?
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
Where does post translational modification occur?
In eukaryotes, but not in prokaryotes
113
What does RNA degradation include?
5' cap removal, shortening of poly A tail, degradation of 5' UTR, coding sequence and 3' UTR
114
What happens if the 5' cap removed?
It is targeted by machinery to degrade RNA, and not translated
115
What happens if the poly A is removed?
The sequence is made unstable and when it arrives at the ribosome it is not translated
116
Why are 3' Poly A tails important?
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
How can alternative splicing produce a non-functional protein?
By placing an early stop codon and producing a truncated protein
118
How were introns discovered?
When parts of RNA sequence did not align with the same DNA sequence
119
What is colinearity?
Strict correspondence between the RNA molecule transcribed and the protein produced
120
What can colinearity indicate?
Deletions or insertions
121
Where were introns first discovered?
Adenovirus
122
How were introns/RNA splicing discovered?
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
What is alternative splicing?
When an intron is excised, sometimes exons are excised with it and once gene can form up to 20 variants
124
Why is alternative splicing important?
Because it allows a single gene to produce several protein products
125
What is an example of alternative splicing?
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
What type of tra do male flies have?
Non functional tra protein, triggers development of male characteristics
127
What type of tra do female flies have?
Longer transcript not including stop codon, functional tra protein and produces female characteristics
128
What is RNA interference?
A regulatory mechanism for translation
129
How are siRNAs and miRNAs produced?
When RNA molecules fold to produce double stranded RNA, which is then cleaved by the enzyme dicer to form smaller fragments
130
How large are siRNAs/miRNAs?
22 base pairs
131
What can siRNAs and miRNAs do?
Inhibit translation by binding with/degrading mRNA
132
How do miRNAs inhibit translation?
One strand combines with proteins to from silencing complex, prevents translation
133
How do siRNAs inhibit translation?
One strand combines with the mRNA and leads to degradation
134
What can some microRNAs do?
Methylate histones or DNA by attaching to sequences and attracting methylation enzymes
135
What is VEGF-A?
Vascular Enthothelial Growth Factor
136
What does VEGF-A do?
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
Why are mitochondira only inherited from the mother?
Forces reduction at every generation in diversity
138
What has happened to some species that have lost chloroplasts?
Some mitochondrial genes are still present in their genomes
139
What can mitochondria and chloroplasts exchange genetic material with?
The nucleus
140
Why have some mitochondrial genes migrated to the nucleus?
So that the nucleus can have full control over the mitochondria, dependent on protein synthesis
141
What are mitochondira dependent on?
Nuclear transcription
142
What do chloroplasts contain?
Circular, double stranded DNA
143
How many base pairs do chloroplast genomes have?
80,000 - 600,000
144
How are chloroplast genomes arranged?
In operons, as in bacteria
145
What type of DNA do chloroplast genomes contain large amounts of?
Non-coding
146
What are chloroplasts similar to?
Eubacteria
147
What are chloroplasts used for?
Assessing phylogenetic relationships
148
What size are mitochondrial genomes?
6000 bp to several million
149
What is the mitochondrial genome associated with?
Proteins similar to histones
150
Where are most mitochondrial proteins encoded for?
The nucleus
151
How do human mitochondrial genomes compare to other species
Quite small
152
What produces free radicals?
Cellular respiration
153
How can free radicals affect DNA?
They damage ir
154
What is heteroplasmy?
Multiple distinct DNA sequences within the cytoplasm of a single cell
155
What is homoplasmy?
Copies of mitochondiral DNA are all identical
156
What is a contig?
A set of overlapping fragments that form a continuous stretch of DNA
157
Where did the idea to sequence the human genome come from?
In the 1980s, many genes had been linked to a variety of physiological processes and diseases
158
What was the aim of the Human Genome Project?
To obtain the entire DNA sequence of the haploid human genome
159
What were the features of the International Human Genome Sequence Consortium?
Headed by Francis Collins, with public funding, free access and started earlier than other projects
160
What method did the IHGSC use?
Mapping overlapping clones method
161
What were the features of the Celera project?
Headed by Craig Venter, private funding
162
What method did Celera use?
Whole genome shotgun technique
163
What was done in the IHGSC strategy?
Human genome partitioned into large sequences and stored in yeast mini chromosomes, then each one sequences and assembled using a genetic map
164
What was done in the Celera strategy?
Small insert clones were prepared directly from genomic DNA and sequenced in a highly automated way
165
Which effort was deemed to be more successful?
Celera, it was cheaper and faster and the shotgun method was used to finish the human genome project
166
What is genomics?
The study of genomes using a variety of tools
167
What is structural genomics?
Determines the DNA sequences of entire genomes, aims to understand the organisation and sequences of genetic information contained within a genome
168
How many genes are in the human genome?
Around 20,000
169
What are transposons?
'Jumping genes', DNA sequences which can change their position in a genome
170
Approximately how much of the genome codes for proteins?
1.5%
171
What is comparative genomics?
Refers to the comparison of genomes to understand evolution of genes and species and the function of genes
172
What are homologs?
Genes that are evolutionarily related
173
What are orthologs?
Homologous genes in different species that evolved from the same gene in a common ancestor
174
What are paralogs?
Homologous genes arising by duplication of a single gene in the same organism
175
What is the difference between orthologs and paralogs?
Orthologs are in the same organism, paralogs are in different organisms
176
How can the importance of a gene be determined by its rate of evolution?
Genes which show accelerated evolution tend to have greater influence
177
What is fundamental genomics?
Determines the functions of genes using genomic based approaches
178
What is the transcriptome?
All the RNA molecules transcribed from a genome
179
What is transcriptomics?
Assessment of gene activity of many genes at a time
180
What are microarrays?
Nucleic acid hybridisation, using a known DNA fragment as a probe to find a complementary sequence
181
What is next generation sequencing?
Sequencing RNA fragments which are then annotated by aligning them to a reference genome sequence
