Genes, genomes, genomics! Flashcards
(140 cards)
1
Q
What does a virus consist of?
A
- Nucleic acid
- Enclosed in a protein coat (capsid)
- Lipid envelope (sometimes)
2
Q
What is a virus described as if it does not have a protein coat?
A
Naked
3
Q
How can a viral genome vary?
A
- DNA or RNA
- Single or double stranded
- Linear or circular
- Haploid or different ploidy level
The type of genome depends on its life cycle
4
Q
Define genome
A
The complete set of hereditary genetic material contained in an organelle, a cell,
or an organism
5
Q
Give the 3 common features of a genome
A
Made of nucleic acids
Self-replicating
Code for something
6
Q
Define virus
A
A virus is one or more nucleic acid molecules within a coat made protein (the
capsid), naked or enveloped by a lipid membrane, which can only reproduce
inside a cell
7
Q
What are the subunits of a capsid?
A
Capsomeres
8
Q
Give an example of a virus with a helical capsid
A
Tobacco mosaic virus
9
Q
Give an example of a virus with an icosahedral capsid
A
Adenovirus
10
Q
What kind of virus has an outer membrane with glycoprotein spikes surrounding the capsid?
A
Influenza virus
11
Q
What kind of virus has a complex shape with an icosahedral head and a tail?
A
Bacteriophage T4
12
Q
What is Phi X 174?
A
The first genome every to be sequenced - a type of bacteriophage that infects E.Coli.
13
Q
Use Covid as an example of why we should study viral genomes
A
Monitoring of new strains
Monitoring spread
Production of RNA vaccines
14
Q
Are prokaryotes usually haploid or diploid?
A
Haploid - one chromosome copy per cell
15
Q
What is a plectoneme?
A
A plectoneme is a supercoiled structure formed when a DNA molecule twists around itself.
It’s a form of DNA supercoiling, often seen in circular DNA like bacterial chromosomes or plasmids
16
Q
How do prokaryotes compact their DNA?
A
Mainly through supercoiling and use of a dense protein scaffold using nucleoid associated proteins
17
Q
What do topoisomerase allow?
A
causes a break in the DNA to allow rotation of the strands
18
Q
What 3 things is supercoiling maintained by?
A
DNA gyrase
Other DNA topoisomerases
NAPs
19
Q
Define metagenomics
A
The study of the genetic material (DNA or RNA) from all organisms within a specific environment, without the need to isolate or culture individual organisms
20
Q
How do eukaryote and prokaryote origins of replication differ?
A
Prokaryote genomes have a single origin of replication
Eukaryote genomes have multiple origins of replication - and therefore many replication forks
21
Q
What is a histone DNA complex called?
A
A nucleosome
22
Q
How are histones arranged in eukaryotic DNA?
A
- DNA wrapped around histones
- histone complexes form nucleosomes
- Nucleosomes wind into a helix
- Chromatin fibre formed into looped domains
- Looped domains fold during metaphase
23
Q
Define euchromatin
A
the fraction of the nuclear genome that contains transcriptionally active DNA and which adopts a relatively extended conformation
24
Q
Define heterochromatin
A
Highly condensed chromatin that shows little or no evidence of active gene expression
25
What are the 2 kind of heterochromatin?
Constitutive: remains condensed through the cell cycle
Facultative: condensation is reversible and usually cell type-specific
26
Define epigenome
The set of chemical modifications to the DNA and DNA-associated proteins in the cell, which alter gene expression, and are heritable (via meiosis and mitosis)
I.E. the packaging
27
What is an example of epigenomics in the female human chromosome? What does it need?
X chromosomes in female cells relies on epigenomic mechanisms
- needs DNA methylates, histone deacetylases and DNA-binding proteins otherwise it is heterochromatic and inactive
28
What is DNA measured in?
Base pairs
29
What is the C value?
(C = Constant or Characteristic)
Amount of haploid DNA per nucleus, usually in picograms
1 picogram ~ 1 Gbp
30
What is the C-value paradox?
Genome size is not proportional to the apparent complexity of an organism
Similar organisms may have greatly differing genome sizes - e.g. canopy plant has larger genome size than humans
31
Approximately how many genes do humans have?
19,396
32
What is an open reading frame?
a region of the genome that is transcribed and has a defined start and
stop codons
33
What does it mean if an ORF is polycistronic?
multiple ORFs under the control of the same regulatory sequences that are
transcribed together
- one promoter controls multiple genes
34
How many transcription start sites does each polycistronic operon have?
1 - ATG
35
What is the Shine-Dalgarno sequence?
(AGGAGG) helps align ribosome to start codon
36
What 3 things is transcription regulated by?
Promoter - Pribnow box
Operator
Terminator
37
Describe a terminator
C & G bases in inverted repeat
* Forms a hairpin loop
* Sequence recognised by Rho (ρ) factor
* Helps terminate transcription
38
Give an example of a large genome.
Paris japonica has a genome size of 150 Gb.
39
Give an example of a small genome.
Carsonella ruddii has a genome size of only 160 Kb.
40
What is gene density?
The number of genes per unit of DNA, typically measured per pg or Mb.
41
What are the three levels of biological information flow?
Genome (DNA), Transcriptome (RNA), Proteome (Protein).
42
What are features of prokaryotic genes?
Often polycistronic, have a single transcription start site, and contain Shine-Dalgarno sequences.
43
What regulates transcription in prokaryotes?
Promoter (−35 and −10 regions), operator sequences, and transcription terminators.
44
What is a Pribnow box?
The −10 region of a prokaryotic promoter (TATAAT).
45
What is a Kozak sequence?
A sequence in the 5′ UTR of eukaryotic mRNAs (ACCATGG) that promotes ribosome binding.
46
Where is the polyadenylation site found?
In the 3′ UTR of eukaryotic genes, it signals addition of a poly-A tail to RNA.
47
What is an enhancer?
A distal regulatory DNA sequence that increases gene transcription by interacting with promoters.
- increases gene expression
48
What are transcription factors (TFs)?
Proteins that bind specific DNA sequences to regulate gene expression.
49
What is the function of the promoter in eukaryotic genes?
It guides RNA polymerase to the transcription start site (TSS).
50
What is the difference between prokaryotic and eukaryotic gene structure?
Prokaryotic genes are often polycistronic and lack introns; eukaryotic genes are typically monocistronic and contain introns.
51
What are gene families?
Groups of related genes that derived from a common ancestor
- may be clustered or dispersed
52
How do new members of gene families arise?
By duplication of a common ancestor gene which creates two identical copies of it
53
Are introns conserved in gene families?
Yes, gene families have conserved intron locations
54
Give an example of a gene family.
The globin gene family (e.g., α-globin, β-globin, γ-globin).
55
What are the sources if gene duplication?
Recombination, retrotransposition, or replication slippage.
56
What does gene duplication create?
New functions
57
What is a paralogue?
A gene related to another in the species by duplication within the same genome/species
e.g human alpha and beta globin
58
What is an orthologue?
A gene in different species that evolved from a common ancestral gene by speciation.
- same function, different species
59
What is an analogue?
Genes that perform similar functions but do not share a common ancestor.
60
What is a homologue?
Genes that share a common evolutionary ancestor.
61
What is meant by conserved intron positions in gene families?
Intron positions that remain in the same location across different genes within a family.
62
How does gene duplication contribute to evolution?
It provides raw genetic material for the evolution of new gene functions.
63
What is the function of the TATA box in eukaryotic promoters?
It is a core promoter element that helps position RNA polymerase for transcription initiation.
64
What is the Initiator (Inr) sequence?
A 17 bp sequence near the TSS that allows transcription initiation without a TATA box.
65
What is the 5' UTR?
The untranslated region before the start codon; helps regulate translation.
contains Kosaz sequence - helps ribosome recognise start codon
- also contains 5' methylated cap
66
What is the 3' UTR?
The untranslated region after the stop codon; involved in mRNA stability and localization.
- contains polyadenylation site
67
How are operons in prokaryotes different from eukaryotic gene expression?
Operons have multiple genes under one promoter; eukaryotes typically express one gene per promoter.
68
What does 'monocistronic' mean?
A transcript that encodes only one protein — typical in eukaryotes.
69
What does 'polycistronic' mean?
A transcript that encodes multiple proteins — typical in prokaryotes.
70
How is gene expression regulated in eukaryotes?
By promoters, enhancers, transcription factors, and epigenetic modifications.
71
What is genomic conservation?
The presence of similar genes or sequences across different species, indicating shared ancestry.
72
What percentage of human genes have orthologues in mice?
Around 80%.
73
What does it mean that most human genes are homologous to other species?
It means they share a common ancestry and often have similar sequences and functions.
74
How many bp is 1kbp?
1000bp
75
How many bp is 1Mbp?
1,000,000bp (I million)
76
How many bp is 1Gbp?
1,000,000,000bp (a thousand million)
77
what is segmented vs non-segmented genetic info?
segmented is where DNA/RNA is split into coding and non-coding segments - exons and introns
non-segmented is all coding regions - exons
78
What is the human C value?
3.2pg (3.2Gbp)
79
how compact are prokaryote genomes?
Relatively small:
160,000 to 12 million bp
Compact:
>85% genome is in protein-coding
sequences or RNA genes
80
What is the genome size of PhiX 174? How many genes?
5Kb, 11 genes
81
What is the genome size of E. coli? How many genes?
4.6Mb, about 4400 genes
82
What is the genome size of H. sapiens? How many genes?
3.2 Gb, about 20,000 genes
83
What is the genome size of Paris Japonica (largest plant genome known)? C-value?
150Gb, C-value = 150pg
84
What is the genome size of Carsonella Ruddii (bacteria)? C-value = 0.0002pg
160Kb, C-value = 0.0002pg
85
What is the average size of a human intron?
200-500bp but can be 100-2000
86
What does splicing do?
Removes introns
87
What kind of modification is splicing?
Pre-translational, changes pre-mRNA into mature mRNA
88
What is the TATA box?
core promoter element in eukaryotes and archaea
- recognised by TATA binding protein
89
What is the initiator?
Simplest functional promoter in eukaryotes
- 17bp
- able to initiate transcription in the absence of a TATA box
- most common sequence at the TSS
90
where do Transciption factors bind?
Enhancer
91
where does RNA polymerase bind?
to the promoter
92
What are some famous transcription factor families?
1. zinc fingers
2. helix turn helix
3. leucine zipper
93
What is prokaryotic regulation done by?
The tryptophan operon
94
How many transcription and translation start sites in the tryptophan operon for prokaryotic regulation?
1 transcription start site
5 translation start sites
95
How many transcription and translation start sites in eukaryotic regulation?
5 transcription start site
5 translation start sites
96
Helpful pic of prokaryotic gene
97
What is the initiator Inr in eukaryote genes?
17 bp
* Simplest functional promoter
* Able to initiate transcription in the absence of TATA box
* Most common sequence at the TSS in eukaryotes
98
What is the TATA box?
Eukaryote promoter - equivalent in prokaryotes is the Pribnow box
Core promoter in archaea and eukaryotes
Recognised by the TATA-binding protein (TBP)
99
What is a tandem repeat/satellite DNA?
Clusters of short repeated sequences
They remain condensed throughout the cell cycle, and are therefore classes as constitutive heterochromatin
100
What is satellite DNA also known as?
Tandem repeats
101
Give 2 examples of satellite DNA
Centromeric DNA
Telomeric minisatellite
102
What is the eukaryotic equivalent of the Shine Dalgarno sequence?
Kozac sequence
103
What is the prokaryotic equivalent of the TATA box?
Pribnow box
104
What are telomeres?
repetitive sequences, with a cluster of Gs on one strand, at the
end of the linear chromosomes that
protect the ends from degradation or
tangling
105
What is a telocentric chromosome?
telomere next to centromere, so just one arm
106
What is an acrocentric chromosome?
p is noticeably shorter than q
107
What is a metacentric chromosome?
p and q are roughly of equal length
108
What are the 3 kinds of chromosome?
Telocentric
Acrocentric
Metacentric
109
What are telomeres important for?
Replication and maintenance
Protect end of chromosome from degradation and damage
Helps determines lifespan and reproductive capacity
110
Why does the telomere get shorter in cell division?
There's no 3' end to extend after RNA primer removal during replication
111
What does a longer telomere show?
More cycles of cell division it can go through
112
How do stem cells lengthen the telomere?
Telomerase uses RNA template (made by primate) to extend the telomere
- telomerase moves to new end and DNA polymerase fills the gap
- repeated to lengthen the telomere
- also used in cancer
113
What are mini satellites?
variable number tandem repeats
- occur at end of genome
- repeating unit is 10-100bp in size
- each can occur 10-1500 times
114
What are microsatellites?
Short tandem repeats
- occur throughout the genome
- repeating unit is 2-6b in size
- each can occur 5-200 times
- can be used for genetic fingerprinting
115
What are interspersed repeats?
Longer sequences that are present in many copies dispersed throughout
the genome. (basically ex-transposons - no longer active and jumping)
- DNA transposons
- RNA transposons:
LINEs
SINEs
LTR retrotransposons
116
What are no longer active transposable elements called?
Interspersed repeats
117
What are the most common kinds of retrotransposons?
LINEs - do encode their own reverse transcriptase
SINEs - use someone else's reverse transcriptase
118
What do LINEs stand for?
Long Interspersed Nuclear Elements
119
What do SINEs stand for?
Short Interspersed Nuclear Elements
120
Details about LINEs?
Transpose via RNA intermediate which is then reverse transcribed
- 21% of human genome
- 5000bp repeat units
- approx. 100 LINEs are active in transposition in human genome (only active in mutagenesis)
121
Details about SINEs?
- use LINE machinery to retrotranspose
- 13% of human genome
- less than 500 bp repeat units
- most found in introns
122
What are 3 examples of SINE families?
Alu (most common) - derived from rRNA
MIR - derived from tRNA
MIR3 - derived form tRNA
123
How were retrotransposons used in maize?
Retrotransposon Hopscotch 1was inserted into TB1 promoter which increase gene expression and led to a single and bigger ear of maize
124
What is a pseudogene?
a fragment of DNA that resembles a protein- coding gene but does not actually encode a protein - was once active in an ancestor - basically gene fossils
125
What is a retrotransposon?
A type of transposable element (a "jumping gene") that can copy and insert into a new location in a genome via an RNA intermediate
- copied into RNA first then reverse transcribed back into DNA and inserted.
126
How is an unprocessed or classical pseudogene created?
generated by accumulation of null mutations
gene product no longer under evolutionary
pressure
- in duplicated genes or unitary genes (single copy gene)
- humans have mostly duplicated pseudogenes
127
How is a processed pseudogene made?
arise from reverse transcribed RNA inserted into the genome
- usually carried over by a retrotransposon
Processed = no processing needed, already spliced mRNA
These are copies of real genes that accidentally got retrotransposed.
Their mRNA was reverse-transcribed and inserted.
They look like genes but don’t work (no introns, no promoter).
128
Explain retrotransposition
Retrotransposition is when a piece of genetic material is copied from RNA back into DNA and inserted somewhere else in the genome.
Steps:
Transcription: A gene or retrotransposon is copied from DNA into RNA (just like normal gene expression).
Reverse transcription: An enzyme called reverse transcriptase converts that RNA back into DNA.
Insertion: The new DNA is inserted somewhere else in the genome
129
How does Sanger sequencing work?
Primer binds to the template DNA.
DNA polymerase starts building the complementary strand.
Occasionally, a ddNTP is added instead of a dNTP, causing the chain to terminate.
This results in fragments of varying lengths, each ending with a ddNTP.
The fragments are then separated by size using capillary gel electrophoresis.
A detector reads the fluorescent label on each ddNTP to determine the terminal base.
The computer reconstructs the DNA sequence from shortest to longest fragments
130
What is Sanger sequencing accurate for?
Short sequences
131
What has long DNA sequencing moved onto?
Next generation sequencing
132
What is next generation sequencing?
Sequeneces many fragments at once
- adaptors are used
- sensors read fluorescent signals and turns them into a letter
133
Why is next generation sequencing good?
- Can sequence a lot of DNA bases at once and faster
134
What are two examples of next generation sequencing?
Illumina novaseq or flow cells (short read or shot gun sequencing)
135
What is 3rd generation sequencing?
Nanopore DNA sequencing
136
What is Nanopore DNA sequencing?
- Electrical current through a nanopore on a flow cell
- Each nanopore has its own electrode
- Nucleotide goes through and disrupts current
- Each nucleotide creates a diff disturbance in electrical signal
- Translated into nucleotide sequences
- Nucleotide is called by basecalling algorithm
137
Advantages of nano pore sequencing?
- Doesn’t require DNA polymerisation (not a DNA synthesis based technique)
- Don’t have to chop up DNA
- No errors, only from interpretation of digital signal
138
What sequencing method is used for ultra long reads?
Oxford nanopore - can even do entire chromosomes
139
How does a unitary pseudogene come about?
Result from a mutation in a single-copy gene that was once functional, but is no longer
140
When did the human genome project finish?
2003, took 13 years
