Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIO3A: Processes 2 Patterns > S1: W4 (Prof. Kelsey) > Flashcards

S1: W4 (Prof. Kelsey) Flashcards

1
Q

Knowing the three acts of a genome: What are the three acts?

A

● Act 1
= Who?

● Act 2
= What?

● Act 3
= Why?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Act 1?

A

= what exactly is a genome? & what can it tell us?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Genome?

A

= complete genetic materials in a DNA molecule of an organism.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Components of a genome generally? (5)

A

• Protein-coding genes
• Non-coding genes.
• Junk DNA.
• Mitochondria & mt genome (eukaryotes).
• Chloroplasts & cp genome (algae & plants).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Eukaryotic genome components? (2)

A

• Repetitive DNA sequences.
• Non-repetitive DNA sequences.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Eukaryotic genomes attributes? (4)

A

• Single copy in haploid genome.
• Repetitive sequences are present in >1 copy.
• Larger genomes don’t have more genes, but more junk/repetitive DNA.
• Non-repetitive sequences are unique.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Junk DNA?

A

= a DNA sequence that has no relevant biological function.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Why is it called Junk DNA?

A

It’s because scientists haven’t designated a specific function to it.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Types of repetitive DNA? (2)

A

• Satellite DNA.
• Interspersed repeats.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Relate level of complexity of organism to DNA?

A

More complex organism, more repetitiveness.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Endosymbiosis attributes? (3)

A

• Responsible for mt & cpDNA.
• Most of the genes of the mt & cp genomes have been transferred to the nucleus, driving the organelle’s evolution.

• Bacterium evolves into mt, losing genes that are necessary for its development.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Why do we have mitochondria? (3)

A

• Help build the organelle’s internal structure.
• Allow localized bioenergetic modulation.
• Less sensitive to hybridization.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Why map a genome? (3)

A

• Individual genomes show extensive variation.
• Where is it? How did it get there?
• Polymorphism found at the phenotype level when a sequence affects the gene functions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Genome mapping types? (2)

A

• Linkage maps.
• Restriction maps.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Genome mapping attributes? (2)

A

• Uses linkage maps.
• Uses restriction maps.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are linkage maps based on?

A

Frequency of recombination between genetic markers.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are restriction maps based on?

A

Physical distances between the markers.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How are genomes mapped?

A

By sequencing their DNA & identifying functional genes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

GWS attributes? (3)

A

• Associate a specific trait with a genotype (SNP).
• Identify SNPs that are more frequently found in patients with a particular disorder.
• SNPs can be associated with genetic disorders/other traits of interest.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Genome sequencing & Evolution attributes? (2)

A

• Differs in the level of complexity/requirements of an organism that enable it to function well.
• No. of genes in bacterial & archaeal genome is proportional to genome size.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How many different types of genes are there?

A

Many genes are duplicated & the no. of different gene families is much smaller than the total no. of genes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Human genome attributes? (4)

A

• Fewer genes than originally expected.
• Genomes occupy 25% of human genome, but protein-coding sequence are only a small part of fraction.
• Exons comprise ~5% of each gene, so genes (exons & introns) are ~25% of the genome.
• Human genome has ~20 000 genes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How many genes are essential for life?

A

We don’t fully understand the persistence of genes that might be unused in the genome as a systematic analysis of loss of function for 86% of worm genomes shows that only 10% have detectable effects on the phenotype.

24
Q

Genomes & Evolutionary questions? (2)

A

• Is organismal diversity due to presence/absence of certain genes?

• Why do mammals, amphibians & plants have larger genomes?

25
Q

Is organismal diversity due to presence/absence of certain genes? (2)

A

• Many gene families are expanded by duplication.
• Coincides somewhat with diversification of Metazoa.

26
Q

Eg of Evolutionary Q1?

A

Teleost fish.

27
Q

Act 2?

A

= What? & speaks on how genomes come in all sizes.

28
Q

Genome size attributes? (4)

A

• Varies a lot.
• Specialized in function.
• Genome size is associated with organisms of high complexity & tighter regulations for cell function.
• Bigger isn’t always better.

29
Q

Larger genomes results/effects? (3)

A

• High chances of aberrations in organisms/more suffering.
• Difficult maintenance.
• Slower development.

*All effects due to high energetic requirements.

30
Q

Why aren’t bigger genomes always better?

A

Explain effects of having larger genomes.

31
Q

Eg of Specialized in function in Genome size?

A

GP vs Specialists.

32
Q

Eg of Why bigger/more genomes aren’t always better?

A

Article of how extra DNA had deformed the bodies, hearts & brains of salamanders.

33
Q

Act 3?

A

= the Why & How of genomes.

34
Q

Gene duplication attributes? (4)

A

• Contributes to genome evolution.
• Slow process.
• Results in gene families.
• Pseudogenes lose their original function.

35
Q

What causes pseudogenes to lose their original function? (2)

A

• Reverse transcription.
• Integration of mRNA transcripts.

36
Q

Cause of non-processed Pseudogenes?

A

Incomplete duplication.

37
Q

Selfish genes?

A

= genes whose only goal is to replicate & be inherited.

38
Q

Selfish genes attributes? (2)

A

• Function is unknown yet.
• Contribute to large parts of junk DNA.

39
Q

Molecular phylogenetic tree?

A

= tree showing relationship between lineages.

40
Q

Molecular phylogenetic tree attributes? (4)

A

• Can be produced using molecular data.
• Based on molecular data.
• General term.
• Lineages might be computed from genome-wide DNA or a single gene.

41
Q

Gene tree?

A

= phylogenetic tree computed from data coming from a single gene.

42
Q

Egs of Gene trees? (2)

A

• COI based tree (plastid marker).
• ITS based tree.

43
Q

Species tree?

A

= phylogenetic tree computed from genome-wide DNA data.

44
Q

Species tree attributes? (2)

A

• An amalgamation of gene trees.
• Based on multiple markers or the entire gene.

45
Q

Egs of Species trees? (2)

A

• Multi-locus tree.
• NGS tree.

46
Q

Gene tree vs Species tree? (2)

A

● Amount of data used.
● Origin of data used.

47
Q

Is a gene tree not just a species tree with fewer data?

A

No.

48
Q

Reasons why gene trees & species trees are incongruent? (4)

A

● Genes can have unequal rate of evolution (divergence often precedes speciation).

● Gene loss & gene duplication are common.

● Gene flow can occur between lineages after their separation.

● Recombination between neighbouring gene regions.

49
Q

Eg of Reason 1?

A

Hypoxis parvula var. albiflora & Hypoxis parvula var. parvula.

50
Q

Explain Eg of Reason 1? (2)

A

• Even though they look different they are related.
• Gene tree shows they’re different but species tree shows that they’re of the same species.

51
Q

Terms to recall for Reason 2? (3)

A

• Homolog.
• Ortholog.
• Paralog.

52
Q

Eg of Reason 3?

A

Rhodohypoxis baurii & Hypoxis parvula.

53
Q

Explain Eg of Reason 3? (2)

A

• Mate regardless of morphological differences & being different species/unrelatedness.
• Gene tree fails to separate species in the occurrence of gene flow but species tree is able to do so successfully.

54
Q

Why care about gene trees at all in phylogenetics/gene trees importances? (5)

A

• Building blocks of species trees.
• To determine the evolutionary history of a gene family.
• Infer gene duplications & losses.
• Estimate bounds of times these events occurred.
• Determine if a given pair of homologs are orthologs or paralogs.

55
Q

What do you mean by “estimate bounds of times these events occurred”?

A

We mean to estimate the speed at which these events occurred & track them.

BIO3A: Processes 2 Patterns (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions