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BI1051 - genetics and evolution > Genes, genomes, genomics > Flashcards

Genes, genomes, genomics Flashcards

(100 cards)

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1
Q

What is a genome?

A

The complete set of hereditary genetic material contained in an organelle, a cell or an organism.

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2
Q

How many different chromosomal molecules are there?

A

24.

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3
Q

What are similar for all genomes?

A

Made of nucleic acids, self-replicating, encode info via transcription/translation.

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4
Q

What is a virus?

A

One or more nucleic acids molecules within a coat made protein (the capsid), naked or enveloped by a lipid membrane, which can only reproduce inside a cell.

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5
Q

What are viral genomes’ characteristics?

A

DNA or RNA, single or double stranded or both, linear circular or both, segmented or not, type depends on life cycle.

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6
Q

What was the first genome to be sequenced?

A

Phi X 174, a bacteriophage or phage that infects E.coli, genes overlap with each other in genome.

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7
Q

Who was the first to complete in vitro DNA synthesis, DNA genome sequenced, genome assembled in vitro respectively?

A

Arthur Kornberg 1967, Fred Sanger 1977, Craig venter 2003.

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8
Q

Why should we study viral genomes and what were important ones studied?

A

Whole genome sequencing for monitoring new strains, monitoring spread, production of RNA vaccines - HIV, SARS-CoV-2.

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9
Q

Who produced a detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing?

A

Prof Thomas Connor.

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10
Q

What are characteristics of prokaryote genomes?

A

Compact, DNA, double stranded, circular, non-segmented, one chromosome (nucleoid) + plasmids.

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11
Q

In what way are prokaryote genomes relatively small and compact?

A

160,000 to 12 million bp, compact as >85% genome is in protein-coding sequences or RNA genes.

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12
Q

How do prokaryote genomes often obtain plasmids?

A

Transfer between cells.

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13
Q

How are prokaryotic chromosomes typically maintained?

A

Generally maintained at one copy per cell i.e. haploid.

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14
Q

How are plectonemes produced?

A

RNA and DNA polymerases will over and underwind prokaryote DNA causing it to deform into plectonemes.

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15
Q

What type of plectonemes does overwinding cause?

A

Positive supercoils.

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16
Q

How do prokaryotes compact their DNA?

A

Through supercoiling.

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17
Q

What are the nucleoid associated proteins?

A

Dense protein scaffold.

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18
Q

How is supercoiling maintained?

A

By DNA gyrase, other DNA topoisomerases, NAPs.

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19
Q

How does modulating supercoiling take place?

A

Unwinding parental DNA, twist form ahead of replication fork, topoisomerase causes transient break to allow rotation of strands.

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20
Q

Why should we study prokaryote genomes - metagenomics?

A

Gut samples from 124 Europeans, 160 species bacteria per person, many special in all samples, some varied person to person, associated with obesity, bowel diseases, even mental health.

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21
Q

What are characteristics of eukaryote genomes?

A

Contained in nucleus, DNA, double stranded, linear, segmented, one or more chromosomes, nucleus, plus organelles own genome (multiple copies per cell).

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22
Q

What’s the difference between prokaryote genomes replication and eukaryotes?

A

Prokaryote genomes have single origin of replication, eukaryotes have multiple origins.

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23
Q

How does genome replication take place?

A

DNA polymerase elongates strands, single stranded binding proteins keep templates separated, DNA helicase unwinds, primase synthesises primer.

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24
Q

How does eukaryote DNA wrap around histones?

A

Each histone complex forms a nucleosome, nucleosomes wind into helix, chromatin fibre form looped domains, fold during metaphase.

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25
What is chromatin?
DNA and protein complex, DNA wrapped around histones proteins and condensed to form fibres.
26
What is euchromatin?
The fraction of nuclear genome that contains transcriptionally active DNA and which adopts a relatively extended conformation.
27
What is heterochromatin?
Highly condensed chromatin that shows little or no evidence of active gene expression.
28
What is constitutive heterochromatin?
Remains condensed through the cell cycle.
29
What is facultative heterochromatin?
Condensation is reversible and usually cell-type specific.
30
What is the epigenome?
The set of chemical modifications to the DNA and DNA-associated proteins in the cell, which alter gene expression and are heritable.
31
What does the inactivation of X chromosomes in female cells rely on?
Epigenetic mechanisms.
32
What scientific questions can be answered by studying genomes?
Number of genes, gene function (fundamentals, disease, breeding), genome function, diversity, evolution, evolutionary relationships.
33
How do we measure genome size?
DNA measured in base pairs (bp).
34
What does 1 base pair =?
1 letter in genetic code (A, T, C, G).
35
How can you convert between 1bp, Kb, Mb, Gb?
1,000,000,000 bp = 1,000,000 Kb = 1,000 Mb = 1Gb.
36
What is the C value when measuring genome size?
C = constant or characteristic, amount of haploid DNA per nucleus, in picograms.
37
How many picograms in a Gbp?
1 picogram ~ 1 Gbp.
38
What is the human C-value?
3.2pg, 3.2 x 10^9 bp of DNA.
39
How do genomes of Phi X 174, E.coli and H.sapiens vary in size?
5Kb 11 genes vs 4.6Mb ~4400 genes vs 3.2Gb ~20000 genes respectively.
40
What is the C value paradox?
Genome size is not proportional to apparent complexity of an organism, similar organisms may have greatly differing genome sizes.
41
What is the relationship between amount of DNA and proteins?
Amount of DNA is not proportional to that required to produce all proteins made by an organism.
42
What is the composition of the human genome?
Repeats 54%, pseudogenes 5%, non-coding 7%, protein coding introns 22%, protein coding exons 2%, other heterochromatin 9%.
43
What is the length of human introns and average human introns?
100-2000bp and 200-500bp.
44
What are the different types of RNAs in the human genome?
Ribosomal RNA (rRNA) genes, transfer RNA (tRNA) genes, small RNAs, long non-coding RNAs.
45
What is gene density?
Number of genes per pg of DNA, highly variable.
46
What is a gene (officially)?
The set of genomic sequences required to encode a particular functional product or set of products which overlap in sequence.
47
What are the first two gene definitions and by who/when?
Basic unit of hereditary info - Wilhelm Johansson 1909, one gene one enzyme on step in metabolism - Beadle and Tatum 1941.
48
What was the encode project definition of a gene and by who/when?
A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products - Gerstein 2007.
49
What is an open reading frame (ORF)?
A region of the genome that is transcribed and has defined start and stop codons.
50
What are important features for ORFs?
Can be polycistronic (multiple under control of same regulator), each operon has single TSS (transcription start site), each ORF has start codon and stop, shine-dalgarno sequence helps align ribosome to start.
51
How is transcription regulated?
Promoter (upstream of TSS, -35 region, -10 region or pribnow box), operator, terminator.
52
What are terminators in prokaryotic gene regulation?
C and G bases in inverted repeat, form hairpin loop, sequence recognised by Rho factor, helps terminate transcription.
53
What are important features for eukaryotic gene regulation?
TSS, start, stop codons, exons and introns, untranslated regions (UTR) at 5’ and 3’ ends, promoter guides RNA polymerase to initiate, enhancers increase expression (distal regulatory sequences).
54
What’s the difference between 5’ UTRs and 3’ UTRs?
5’ = 5’ methylated cap, contains Kozac sequence equivalent to shine-dalgarno in pros, 3’ = contains poly adenylation site.
55
What are characteristics of eukaryote human intron?
100-2000bp, average 200-500, few short introns, locations vary between genes, gene families often have conserved intron locations.
56
What is the TATA box in Euk gene regulatory sequences?
TATAWAW (W = A or T), core promoter in archaea and eukaryotes, recognised by TATA-binding protein (TBP).
57
What is the initiator (Inr) in Euk gene regulatory sequences?
17bp, simplest functional promoter, able to initiate transcription in absence of TATA box, most common sequence at TSS in euks.
58
What are transcription factors (TFs)?
Proteins that recognise specific regulatory sequence and help modulate transcription (also found in pros).
59
What is the enhancer is Euk gene regulatory sequences?
Has three binding sites each called distal control elements that activator proteins bind to and are grouped by.
60
What is kozac in the Euk gene regulatory sequence?
ACCATGG part of start, ribosomal binding site.
61
How does the tryptophan operon compare to Euk genes?
Continuous segment on one chromosome, transcription = one start site, translation = five start sites, five genes carried on different chromosomes = five start sites for both.
62
Is the human genome unique?
Vertebrates genomes really similar, around 80% human genes have direct equivalent (orthologue) in mouse, <1% human genes have no related genes on other species, high gene conservation among euks.
63
How can genes be single or multiple copies?
Single copy - can occur once per haploid genome, multiple identical - encoding very abundant products (e.g. histones, rRNA).
64
What is a gene family?
Most Euk gens belong to one, i.e. family of genes all from common ancestor, members may be clustered or dispersed.
65
What is an example of a gene family?
Globin gene family - embryonic haem, foetal haem, adult haem.
66
What do most new members of gene families arise from?
Duplication of an existing gene, which is defined as any duplication of DNA that contains a gene.
67
What are sources of duplication?
Recombination, retrotransposition events, replication slippage.
68
What are analogues?
Genes that share a function but not a common ancestor e.g. histones.
69
What are homologues?
Genes that share a common ancestor e.g. globin genes.
70
What are orthologues?
Two homologous genes arising as a result of species divergence.
71
What are paralogues?
Two homologous genes arising as a result of gene duplication.
72
How much of the human genome does repetitive DNA make up?
Half - but can make up majority of genome in some species.
73
What are tandem repeats?
(Or satellite DNA), clusters of short repeated sequences, remain condensed through cell cycle.
74
What is the centromere?
Constricted region of a chromosome where spindle fibres attach during cell division.
75
What are telomeres?
Repetitive sequences at the end of the linear chromosomes that protect ends from degradation or tangling.
76
What are the two arms of chromosomes?
p - short petite and q - long.
77
What are the three types of chromosomes?
Telocentric (telomere next to centromere, one arm), acrocentric (p shorter than q by a lot), metacentric (p and q roughly equal length).
78
What are chromosomes by definition overall?
Linear fragments of DNA.
79
What do tandem repeats - telomeres do?
Protect ends of chromosomes, critical role in replication and maintenance, overhang loops back on itself to form circular structure, repeats of ssDNA sequence with cluster of Gs on one strand (TTAGGG), important to determine lifespan and reproductive capacity, insight into aging and cancer, protective loop to prevent damage.
80
What % of cancers express telomerase?
>90%.
81
What are mini satellites or variable number tandem repeats?
Occur at ends of genome, size of repeating unit 10-100bp, each can occur 10-1500 times, unknown function.
82
What are microsatellites or short tandem repeats?
Occur throughout genome, size of repeating unit 2-6bp, each occurs 5-200 times, used for genetic fingerprinting.
83
What are interspersed repeats?
Longer sequences that are present in many copies dispersed throughout genome - DNA/RNA transposons, LINEs, SINEs, LTR retrotransposons.
84
What are transposable elements, what do they do?
Also jumping genes/transposons, can change position in genome, can mutate (no longer active = interspersed repeats).
85
What do human transposons have?
A truncated or mutated transposase.
86
What are the two main types of transposition?
Cut and paste (non-replication) - class II DNA transposons and copy and paste (replicative) - class I retrotransposons.
87
What are LINEs - long interspersed nuclear elements?
Transpose via RNA intermediate which is reverse transcribed, 21% of human genome, 5000bp repeat units, approx 100 are active in transposition in human genome.
88
What are SINEs - short interspersed nuclear elements?
Use LINE machinery to retro transpose, 13% of human genome, <500bp repeat units, most found within introns.
89
How was retrotransposons responsible for maize domestication?
Insertion in promoter of plant gene increased expression and led to production of single and bigger flower.
90
How can transposons be a source of genomic variability?
Are built-in mutagens.
91
What is a pseudogene?
A fragment of DNA that resembles a protein-coding gene but does not actually encode a protein, DNA fossils - once active in ancestral species.
92
What are unprocessed or classical pseudogenes?
Generated by accumulation of null mutations, product no longer under evolutionary pressure, occur in duplicated genes or single copy (unitary), have ~3800 in humans.
93
What are processed pseudogenes?
Arise from reverse transcribed RNA inserted into genome, usually carried over by a retrotransposons, humans have ~10700.
94
How was sequencing first developed in history?
Frederick Sanger, radioactivity used in 1975, dideoxynucleotides in 1977, <500 bp DNA per 10ths in 1995, commercialised in 1986 by applied biosystems.
95
What was Sanger sequencing?
Sanger chain termination in one reaction, based on fluorescence, 2000- 5000bp per 10hrs, chromatogram, sequencing gel, upped to 500bp per 10hrs in <1995.
96
What was the second and third generation sequencing respectively?
Massively parallel DNA sequencing, nanopore DNA sequencing.
97
How does nanopore sequencing work?
Flow cell with tiny holes, each has own electrode which measures current, nucleotide through pore disrupts current, nucleotide called base calling algorithm.
98
What are the steps for assembling a genome?
Raw accurate long reads (error correction), corrected reads (assembly), initial assembly graph (+ultra long reads), ultra long assembly graph (+long range data), final assembly.
99
What was the human genome project?
Ran from 1990-2003, 8% not readable at time, new methods, better computational approaches.
100
When was the complete human genome map completed?
2022.

BI1051 - genetics and evolution (15 decks)

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