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Principle of genetics > Lecture 6 > Flashcards

Lecture 6 Flashcards

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Biology 101 flashcards
1
Q

Genome

A

The whole hereditary information of an organism that is encoded in the DNA

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2
Q

Human Genome Project

A
  1. Identify 100,000 genes
  2. Determine sequence of the 3B bases human DNA
    3.
    4.
    5.
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3
Q

Heterochromatin

A

Condensed Chromatin

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4
Q

Euchromatin

A

More diffuse chromatin, corresponds to regions where most most genes and functional elements reside

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5
Q

Benefits of Human Genome Research

A
  • improvements in medicine
  • microbial genome research for fuel and environmental cleanup
  • DNA forensics
  • improved agriculture and livestock
  • better understanding of evolution and human migration
  • more accurate risk assessment
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6
Q

-omics Science

A
  • Structural genomics: mapping and sequencing
  • Functional genomics: how genes function
  • Proteomics: how proteins and encoded and function
  • Metabolomics: how small molecules are metabolized and function
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7
Q

Hierarchical shotgun sequencing

A

Break DNA into smaller fragments, sequence each with Sanger seq, assemble contigs to find the whole sequence

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8
Q

Sanger Sequencing

A
  • DNA is fragmented and cloned to a plasmid vector
  • Sequencing reaction using dideoxynucleotides
  • Separation of molecules by electrophoresis
  • Detection of dye-labelled fluorescent tags
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9
Q

Sequence detection technologies

A
  • Sanger sequencing
  • 454 pyrosequencing
  • Illumina sequencing
  • SOLiD sequencing
  • Ion Torrent sequencing
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10
Q

Type of information gleaned from sequencing genomes

A
  • A-T and G-C Content
  • Number of protein coding genes
  • Number of non-coding RNAs
  • Frequency and types of repetitive elements
  • Comparison between physical and genetic distance
  • Homology to other organisms, evolution of genes
    • New genes
    • Duplicated genes
    • Deleted genes
    • Degree of conservation
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11
Q

Syntenic regions

A

Same gene structure between species

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12
Q

Homologs

A

Orthologs or Paralogs

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13
Q

Orthologs

A

Similar genes in two organisms that arose in a common ancestor

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14
Q

Paralogs

A

Similar genes which arose by duplication in the same organism

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15
Q

What is in the human genome

A
  • Protein coding regions (exons)~1.5%
  • Regulatory regions (promoters, enhancers)~5%
  • Repetitive elements (LINEs, SINEs, transposons)~50%
  • Non-coding RNAs ???
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16
Q

Mitochondrial genome unique region

A

Control region (at 12 o’clock)

17
Q

Which pathway are the mtDNA encoded proteins into

A

Electron Transport Chain

18
Q

Classes of interspersed repeats in the human genome

A
  • LINEs
  • SINEs
  • Retrovirus-like elements
  • Transposon
19
Q

Categories of Genetic Variants

A
  • Single Nucleotide Polymorphism
  • Insertion/Deletion
  • Simple Sequence Repeat
  • Copy Number Variation/Copy Number Polymorphism
  • Complex variant
20
Q

How SNPs can be detected by microarrays

A

With differential hybridization (if mismatch, raising temperature denature)

21
Q

Types of Human DNA Variation

A 
Insertion-Deletion polymorphisms:
  - Minisatellites
  - Microsatellites (STRs)
Single Nucleotide Polymorphisms (SNPs)
Copy Number Variations (CNVs)
Others: Chromosomal or large scale variations, rearrangements, translocations, ...
22
Q

Minisatellite

A

Tandemly repeated 10-100bp blocks of DNA => VNTR (Variable Number of Tandem Repeats)

23
Q

Microsatellite

A

Short Tandem Repeat: di-, tri-, tetra-nucleotide repeats

24
Q

Single Nucleotide Polymorphism

A

Frequency of 1 in 10^3 bp, PCR-detectable marker

25
Q

Copy Number Variation

A

Variation in segments of genome from 200bp to 2Mb, once to many copies, detected by array comparative genomic hybridization

26
Q

Gene family

A

Genes with high sequence similarity (>85%) that may carry out similar but distinct functions.
Arise through gene duplication => Mechanism behind evolutionary change

27
Q

Date of shift in sequencing technology

A

2006-2007

28
Q

NGS technology

A

massive parallelization of sequencing reactions producing orders of magnitude more sequence data than capillary-based seq

29
Q

Why sequence more human genomes

A
  • Genetic variation at individual, family and population level
  • Discovery: Heritability of most disease not understood, individual rare variation important
  • Advance medical treatment
30
Q

GINA

A

Genetic Non-Discrimination Act (2008): Research DNA not release to health insurance and workplace (but life insurance, disability and long-term care insurance)

Principle of genetics (9 decks)

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