BioPsych PSYC20006 Theme 4 > Genetics 1 > Flashcards

Genetics 1 Flashcards

(42 cards)

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1
Q

What are the building blocks of genetic code?

What are proteins, what determines their function, and what are their building blocks?

A

Nucleotides or bases:

Building blocks of the genetic code

  • Adenine (A); Cytosine (C); Thymine (T); Guanine (G)

Amino Acids

Building blocks of proteins

  • Represented by specific sequence of three bases
    • Codons
  • Function of a protein is determined by its structure
  • Structure of a protein is determined by its sequence of amino acids
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2
Q

How many bases are there in the whole human genome and how many genes code for protein?

A

Bases:

3 billion bases

Genes that code for protein:

20–25 thousand genes

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3
Q

What is the helix of DNA? What do they carry?

A

Double-stranded. The two strands carry redundant information.

Each base has a partner on the other strand

  • Cytosine pairs with Guanine (C–G)
  • Adenine pairs with Thymine (A–T)
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4
Q

How is DNA bundled? What is the human karyotype comprise of?

A

DNA is bundled in chromosomes

  • The human karyotype comprises 46 chromosomes:
    • 22 pairs of autosomal chromosomes (1–22)
    • Two sex chromosomes (XX or XY)
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5
Q

What determines the structure of protein?

A

Structure of a protein is determined by its sequence of amino acids

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6
Q

What happens when we change a single bases in a codon? What is the caveat?

A

Changing Bases

  • Changes the amino acid
  • Change structure of protein
  • Change function of protein

Caveat

Not necessarily, as each amino acid might has multiple possible codons

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7
Q

What is a single-nucleotide polymorphism (SNP)? What are the different bases called?

A

SNP

  • Position on the genome at which the bases (nucleotide) differs between individual
  • The two alleles of a SNP are the alternative bases
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8
Q

What determines a person’s genotype at SNP?

A

Determined by the two alleles on the two copies of thechromosome

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9
Q

What is phenotype? What kinds are there?

A

Phenotype is the presence, absence or value of a trait of interest

E.g.

  • Psychological diagnosis (binary)
  • Parenting style (categorical)
  • IQ (quantitative)
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10
Q

What are the 5 genetic variants?

A
  1. SNP
  2. Insertion–deletion
  3. Block substitution
  4. Inversion
  5. Copy number
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11
Q

Describe Genetic Variant 0.

A

SNP: Single Base differ

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12
Q

Describe Genetic Variant 1.

A

Insertion–deletion variant

  • Bases added or missing
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13
Q

Describe Genetic Variant 2.

A

Block substitution

  • Multiple bases substituted
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14
Q

Describe Genetic Variant 3.

A

Inversion variant

  • Bases replaced with reversed sequence from other strand
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15
Q

Describe Genetic Variant 4.

A

Copy-number variant

  • Sequence of bases repeated one or more times
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16
Q

What is the difference between mutation and polymorphism?

A

Mutation:

Rare (<1% allele of population)

Polymorphism:

Common (1%/>1% allele of population)

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17
Q

Male vs Female chromosome. What is the extra step?

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A

Female: XX

Male: XY

  • In females, to avoid excess X-chromosome protein, one copy of X in each cell is silence/inactivate
    • This process is random in all mammals
18
Q

How does one copy of X get inactivated?

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A
  • XIST gene
    • RNA transcript
      • Coats one chromosome to be inactivated as a Barr body
  • TSIX gene, on other chromosome
    • RNA transcript
      • Suppresses transcription of XIST
  • TSIX antisense partner of XIST
    • Encoded by same stretch of DNA; transcribed in opposite directions
19
Q

What is gene equation?

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A

P = G + E + GxE + 2cov(G,E)

  • P: Phenotype Variance
  • G: Geneotype Variance
  • E: Environment Variance
  • GxE: Variance from gene–environment interactions
  • 2cov(G,E): Covariance between genes and environment
20
Q

What is the heritability equation?

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A

h2 = G / P

Therefore, proportion of variance in the phenotype that can be attributed to variance from genes

21
Q

Define heritability?

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A

Heritability is the proportion of the phenotypic variance due to genetic causes

22
Q

What kind of measurement is heritability based on?

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A
  • Local measurement
    • Valid for specific population at a specific time
      • Depends on the amount of genetic and environmental variation present in the population
      • Cannot generalise heritability across populations…
23
Q

Describe the Heretability of some disorders?

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A

High

  • Autism
  • ADHD
  • Schizophrenia
  • Biopolar
  • OCD

Low

  • MDD
  • Anxiety
  • Alcohol
  • Eating disorders
    *
24
Q

How do we measure heritability pre-molecular genetics? What fact do we make use of?/

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A

Genetic epidemiology

  • Related individuals share a predictable amount of genetic material
25
Example of genetic epidemiology?
_Twin studies: Concordance rates_ * Higher concordnace in MZ (identical genetics) than DZ (half genetics) suggests genetics component
26
What are models of inheritance?
* Dominant vs Recessive * Autosomal vs X-linked
27
Describe Dominant vs recessive.
_Dominant traits_ Mutation on one copy of chromosome for expression of the phenotype _Recessive traits_ Mutation on both copies (or only copy) of the chromosome
28
Describe Autosomal vs X-linked\*.
* Autosomal traits are carried on the autosomal chromosomes (1–22) * X-linked traits are carried on the X chromosome
29
How can we infer modes of inheritance?
Modes of inheritance can be inferred from a pedigree chart * Black = Affected * White = Unaffected * Circle = Female * Square = Male * Slash = Deceased
30
Describe the Pedigree Chart Reading.
*See Picture* _Main Ideas_ Dominant * Cannot skip * 2 Unaffected Parents cannot have affected offspring Recessive * Can skip * 2 Affected parents cannot have unaffected offspring X-Linked * Cannot transfer father to son * (Recessive) More common in males * (X-Linked + Dominant) Daughter of affected father must be affected, but father of affected daughter may not be affected * (X-Linked + Recessive) Father of affected daughter must be affected
31
What is an example of a mongenic disorder?
Fragile-X (Originated from single gene)
32
What is the gene alteration of fragile-X?
_Copy-number variant_ * in 5′-untranslated region (contains promotor region where transcribing begins) of gene FMR1 * FMR1 essential for synaptic plasticity/learning * expanded CCG sequence triggers _methlyation_ * _​_constricts X chromosome, causing 'fragile' appearance * methyldated promotor region prevents transcription of the gene
33
What are Polygenic disorders? Are they common?
Many genes with small contribution. Monogenic disorders (Fragile-X) are the exception to the rule in behavioural and psychiatric genetics: No single gene for schizophrenia, autism, bipolar disorder, depression or anxiety
34
What does GWAS do?
_Genome-wide association studies_: * Examine statistical association between a *phenotype* and *many SNP markers* throughout the genome * 500,000 - 2,000,000 markers
35
What is linkage disequilibrium (LD) and what does it allow us to do? What can chromosomes be thought of ?
* Association of alleles at different loci in a population is _non-random_ * _​_Chromosomes are mosaics (inherited together in chunks), and hence many variants are correlated * Allows us to observe indirect associations
36
What is a direct association and indirect association in GWAS?
_Direct association_ * Phenotype has a functional association with a genotyped (measured) SNP _Indirect association_ * Phenotype has a functional association with a non-genotyped SNP that is in LD with a genotyped SNP
37
What is allelic dosage model and allelic association model?
_Allelic dosage model_ Quantitative traits Is there a statistical association between the phenotypic measurement and the number of copies of the minor allele? _Allelic association model_ Categorical and Binary traits Is one of the two alternative alleles statistically over-represented in a phenotypic group?
38
What summarises the results of all GWAS tests of association?
_Manhattan plot_ * Each point represents outcome of test for **ONE** snp * x-axis * Physical location on genome and within a chromosone * y-axis * Transformed p value * Lower p value = higher on axis = stronger association
39
What are the thresholds for significance in GWAS?
Stringent, due to multiple comparisions increasing type 1 error * a * Corresponds to Bonferroni correction for ~1 million independent (uncorrelated) tests
40
What predicts genotypes at nongenotyped SNPs?
Imputation * Relies on data from a reference panel of individuals genotyped at high density * Applies patterns of linkage disequilibrium discovered in the reference panel
41
What is the term defining "extent to which a sequence is maintained across species"?
Conservation * High conservation = Important function for evolution
42
What helps to define the region likely to contain the functional variant in a SNP (Other than LD)?
* Genetic distance * Recombination rate * Frequency with which two markers are inherited together
BioPsych PSYC20006 Theme 4
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