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APS 138: Molecular and cell biology > Lecture 7: Genomes and their evolution > Flashcards

Lecture 7: Genomes and their evolution Flashcards

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1
Q

Genome:

A

is the complete set of genes in an organism or the total genetic content in one set of chromosomes

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2
Q

Genomics:

A

is the study of whole sets of genes and their interactions

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3
Q

Comparative genomics:

A

is the analysis & comparison of genomes from different species

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4
Q

Genome sequencing: most ambitious sequencing project to date:

A

the Human Genome Project which began in 1990 and was completed by 2003

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5
Q

Genome sequencing:

Chimpanzee genome was completed by

A

2005 & today many more genomes have been completely sequences

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6
Q

Human genome sequencing project originally took

A

13 years at a cost of $1 billion

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7
Q

In 2008 Illumina sequencing of human genome costs

A

$350,000

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8
Q

in 2014 Illumina annonced they could sequence human genome for

A

$1000

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9
Q

It is now possible to generate hundreds of gigabases of data very quickly, however:

A

assembling genomes and annotated genomes still takes a long time.
- Computational and bioinformatic analyses lag behind our ability to generate data.

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10
Q

How many genomes have been sequenced to date? By 2016..

A

the genomes of more than 14,000 different organisms had been sequenced and another many more are in the process of being sequenced.

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11
Q

Many of the sequences genomes are

A

bacterial & archeal genomes. Approx 10& are eukaryotes, an include vertebrates, invertebrates, protists, fungi & plants

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12
Q

Where are genomes sequenced?

A
  • Genomes are sequenced by a variety of public and private organisations e.g.
    – National Human Genome Research Institute (NHGRI)
    – The Institute for Genomic Research (TIGR)
    – The Wellcome Trust Sanger Institute
    – JGI – DOE Joint Genome Institute
    – Private companies e.g. Syngenta/Monsanto
    – Research lab in Universities, Research Institute
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13
Q

How is genome sequencing prioritised?

A

• The priority-setting process is based on the medical, agricultural and biological opportunities expected to be created by sequencing a given organism

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14
Q

Genomes vary in:

A

SIZE

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15
Q

genomes of most bacteria range from

A

1 to 6 million base pairs (Mb)

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16
Q

Eukaryotic genomes are __ than bacteria

A

larger

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17
Q

most multicellular animals & plants have genomes with at least

A

100 Mb

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18
Q

fruit fly genome has how many base pairs?

A

165 Mb

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19
Q

Human genome number of base pairs

A

3,000 Mb

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20
Q

The genome of the single- celled yeast S. cerevisiae has about __ Mb

A

12 Mb

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21
Q

Within each kingdom/domain there is __ systematic relationship between _____ & ____

A

no
genome size
phenotype

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22
Q

Genomes vary in the number of

A

genes they contain

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23
Q

Free-living bacteria and archaea have ___ genes

A

1,500 to 7,500

24
Q

The number of genes in eukaryotes ranges from

A

about 5000 (e.g. the unicellular yeast) to at least 40,000 genes in multicellular eukaryotes

25
Q

The number of genes is / is not correlated with genome size

A

IS NOT

e. g.
- the nematode worm C. elegans has 100 Mb genome and 20,000 genes
- Drosophilahas165Mb genome and 13,700 genes

26
Q

Eukaryotic genomescna produce more than one polypeptide per

A

gene because of alternative splicing of RNA transcripts

27
Q

Gene diversity:

A

the number of genes presenting a given length of DNA

28
Q

In bacterial genomes most of the DNA consists of

A

genes coding for proteins, tRNA or rRNA

29
Q

Most eukaryotic DNA does

A

not code for protein and is not transcribed into functional RNA molecules.

30
Q

Humans have ___ times as much noncoding DNA as bacteria

A

10,000

31
Q

Multicellular eukaryotes have introns and a vast amount of

A

non-protein coding DNA between genes.

32
Q

“junk DNA” is thought to play important roles in the cell for example

A
  • For example, the genomes of humans, rats, and mice show high sequence conservation for about 500 noncoding regions.
  • The sesequences are more highly conserved than protein-coding genes in these species
33
Q

Only __ of the human genome codes for proteins or produces rRNAs and tRNAs

A

1.5%

34
Q

Gene-relatedregulatory sequences and introns account for, respectively __% and __% of the human genome.

A

5%

20%

35
Q

Intergenic DNA is

A

Noncoding DNA found between genes

  • Pseudogenes
  • Repetitive DNA
36
Q

Pseudogenes are

A

former genes that have accumulated mutations and are nonfunctional

37
Q

Repetitive DNA is

A

is present in multiple copies in the genome

38
Q

About __% of repetitive DNA is made up of transposable elements

A

44%

39
Q

Comparative genomics

A

is the analysis and comparison of genomes from different species

40
Q

Comparative genomics allows us to

A
  • Gain a better understanding of how species have evolved
  • Help explain how the evolution of development leads to morphological diversity
  • Determine the function of genes and non- coding regions of the genome
41
Q

Genome researchers look at many different features when comparing genomes:

A

– sequence similarity,
– gene location,
– the length and number of coding regions (exons) within genes,
– the amount of noncoding DNA in each genome,
– highly conserved regions maintained in organisms
as simple as bacteria and as complex as humans.

42
Q

comparative genomics involves the use of

A

computer programs that can line up multiple genomes and look for regions of similarity among them.
Some of these sequence-alignments tools are accessible to the public over the Internet.

43
Q

Comparative genomics can begin to address a range of questions e.g.

A
  • Which sets of genes are common to many different organisms, or groups of organisms.
  • Which genes are unique?What do these genes do?
  • Which genes are necessary for multicellular life forms; which set of genes are only found in multicellular organisms but not in unicellular ones?
  • Where and how have new genes emerged in evolutionary history?
44
Q

Genome comparisons of distantly related species help us

A

understand ancient evolutionary events

45
Q

Genome comparisons of closely related species help us

A

understand recent evolutionary events

46
Q

Highly conserved genes that have changed very little over time help clarify relationships among species that

A

diverged from each other long ago.

47
Q

Archaea and bacteria diverged from each other between

A

2 & 4 billion years ago - know this form DNA sequencing

48
Q

Highly conserved genes can be studied in one model organism, and the results

A

applied to other organisms

49
Q

Orthologs are

A

Orthologs are genes in different species that evolved from a common ancestral gene by speciation.
• Normally, orthologs retain the same function in the course of evolution.

50
Q

60 percent of genes are conserved between

A

the fruit fly and humans - The two organisms appear to share a core set of genes

51
Q

When Scientists inserted human gene associated with early-onset Parkinson’s disease into fruit flies

A

they displayed symptoms similar to those seen in humans with the disorder.
-Thus control of expression of this gene may be similar between the 2 organisms raising the possibility that Drosophila could act as a new model for testing therapies aimed at Parkinson’s.

52
Q

Researchers have compared the human genome with the genomes of the

A

chimpanzee, mouse, rat, and other mammals.

  • Identifying the genes shared by these species but not by non- mammals provides clues about what it takes to make a mammal.
  • Identifying the genes shared by chimpanzees and humans but not by rodents gives information about primates.
53
Q

In single-base substitutions, chimp and human genomes differ by only

A

1.2%

54
Q

chimps &humans:

Longer stretches of DNA show a ___% difference due to

A

2.7%

insertions or deletions of larger regions in the genome of one or the other species.
– Many of the insertions are duplications or other repetitive DNA.

55
Q

A __ of the human duplications are not present in the chimpanzee genome and some contain regions associated with human diseases.

A

third

  • Transcription factors regulate gene expression and thus play a key role in orchestrating the overall genetic program.

APS 138: Molecular and cell biology (15 decks)

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