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Genetics > Practical 1 > Flashcards

Practical 1 Flashcards

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Biology 101 flashcards
1
Q

How long were contemporary primates on Earth for?

A

35 million years.

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2
Q

What did humans diverge from 4-5 million years ago?

A

The ancestor of our closest primate relatives - chimpanzees.

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3
Q

What happened next?

A

Human-like primates, still with an ape-like body shape spread throughout Africa.

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4
Q

What appeared in Africa around 2 million years ago?

A

Homo ergaster

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5
Q

Which animals emigrated from Africa around 1.8 million years ago?

A

Homo ergaster or a closely related variant - Homo erectus.

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6
Q

What is evidence for this?

A

Skeletons of Homo erectus have been found all over Eurasia as far as China and Java.

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7
Q

Based on observations, palaeontologists formulated a theory of human evolution called the multiple origin model.

This appears not to be true and has no serious advocates today.

What did this state?

A

Major human races split from one another at the time of the H. erectus dispersal from Africa.

These groups evolved separately (with some gene mixing) at many independent sites into modern humans.

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8
Q

The second theory of human evolution is the out-of-Africa replacement (OAR) hypothesis and is broadly accepted today.

Explain the model.

A

Anatomically modern humans (Homo sapiens) evolved first in Africa, probably from H. erectus about 250000-350000 years ago.

A small part of this group colonised Eurasia and the rest of the Earth migrating from Africa in a major expansion about 70000 years ago with a small population of 60-1000.

The expansion of the H. sapiens drove local populations of H. erectus and later H. neanderthalensis to complete extinction with only a small amount of gene exchange (e.g. 1-4% of European and East Asian genomes is estimated to be derived from H. neanderthalensis).

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9
Q

Give 3 pieces of evidence for the OAR hypothesis.

A

Genetic diversity in African populations of humans is far greater than other human populations suggesting the African population is the oldest because it has had longer to accumulate genetic variations.

Large genetic variability in African populations has been shown for mtDNA, Y chromosome polymorphisms and minisatellite sequences (small sequences on DNA not coding for proteins) on autosomes.

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10
Q

2nd

A

The maternal inheritance of mtDNA traced back to African origins and genetic markers on Y chromosome leads to African ancestry for H. sapiens.

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11
Q

3rd

A

Variation in inheritance of genetic markers found closely linked on chromosomes determined the age of a non-African population of humans is only about 100000 years old.

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12
Q

How long are Alu elements?

A

300 base pairs.

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13
Q

Where do Alu elements derive their name from?

A

A single recognition site for the endonuclease AluI, located near the middle of each element.

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14
Q

What is the most abundant sequence in the human genome?

A

Alu element.

Human genome = 1 million Alu elements = 10% of genome.

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15
Q

Where are Alu elements mainly found in the genome?

A

Non coding intragenic (within a gene) regions such as introns.

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16
Q

The Alu element used in our study is in locus CD4 on chromosome 12.

What is a locus?

A

A specific, fixed position on a chromosome where a particular gene is located.

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17
Q

Alu+ = Alu element at this locus
Alu- = Absence of Alu element

What percentage of the African human population is the Alu+ allele found in?

A

82%

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18
Q

Given the information above, why has the deletion of the Alu element occurred?

A

Due to divergence of humans from the great apes.

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19
Q

What is an STR?

A

A short tandem repeat.

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20
Q

The second polymorphic marker in the experiment was an STR consisting of a block of five nucleotides = TTTTC. How many alleles does this locus have?

A

12

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21
Q

How does each allele vary?

A

Depends on how many times block of nucleotides is repeated.
Can be between 4 and 15 times.

22
Q

Only three of these alleles are seen in the human population outside of Africa at a frequency of greater than 10%.
These are STR85 (5 repeats), STR90 (6 repeats), STR110 (10 repeats) alleles.

All great ape species have very limited polymorphism at this locus (3 or 6 repeats).
What does this suggest?

A

Most of the STR polymorphic human alleles appeared after humans diverged from great apes.

23
Q

In the experiment why are oligonucleotide primers flanking the Alu insertion site used to amplify either a 661bp fragment or a 438bp fragment?

A

661bp fragment = Alu element is present.

438bp fragment = Alu element deleted.

24
Q

Because humans are diploids and contain 2 copies of chromosome 12, three genotypes are possible.
List them and state what their PCR products would be.

A

Homozygous Alu+, one PCR product 661bp long.

Homozygous Alu-, one PCR product 438bp long.

Heterozygous for presence of Alu, two PCR products (one 438bp long and other 661bp long).

25
Q

How were the STR markers amplified?

A

Primers TT-F and TT-R that are approximately 30bp from the STR locus.

25
Q

How is it determined which STR allele is present and whether both chromosome 12 carry this allele?

Alleles amplified:
STR80 = 80bp
STR85 = 85bp
STR90
STR100
STR110
STR115
STR120
STR125
STR130

A

The size of the PCR product generated.

The alleles will be resolved by high-resolution agarose gel electrophoresis.

26
Q

What was the source of DNA?

A

Saliva.

27
Q

Why was saliva placed in a hot block at 98 degrees Celsius for 2 minutes before PCR?

A

Primarily to lyse cells and inactivate enzymes that might interfere with the PCR reaction.

28
Q

Why was the saliva and the dilution buffer placed in the microfuge for 10 seconds after using the vortex to mix?

A

To collect the liquid to the bottom of the tube for pipetting.

29
Q

Why was dilution buffer added to the saliva?

A

To help stabilize the sample (Mg2+), facilitate DNA release (lyse cells), and optimize the conditions for the PCR process (pH).

Optimal PCR Conditions:
PCR reactions are sensitive to ionic strength and other solution conditions. A dilution buffer can normalize these factors, ensuring that the DNA sample doesn’t inhibit PCR due to high viscosity, variable salt concentration, or other potential contaminants present in saliva.

30
Q

Why were samples stored on ice before PCR?

A

Keeping saliva samples on ice before PCR is a crucial step to inhibit enzymatic activity (with enzymes that can degrade DNA), reduce growth of microbes that may contaminate sample and maintain sample quality (reduce viscosity).

31
Q

There were 37 cycles, why were the initial cycle and end cycles longer?

A

The longer durations for the start and end of PCR cycles are necessary to ensure complete denaturation of the DNA at the beginning and thorough extension of the DNA strands at the end.

These extended times enhance the overall efficiency and yield of the PCR process, resulting in a more successful amplification of the target DNA.

32
Q

Why were the DNA extracts destroyed after the practical?

A

To prevent contamination, misuse, and storage complications.

33
Q

All humans can be differentiated by very few qualitative characters.
What are qualitative characters determined by?

A

Genetic differences or environmental effects.

34
Q

What is polymorphism?

A

The occurrence in the same locality of two or more discontinuous forms of a species in such proportion that the rarest of them cannot be maintained solely by recurrent mutation.

35
Q

What is the Hardy-Weinberg equilibrium?

A

A hypothesis relating the frequency of alleles in a population to the frequency of particular haploid and diploid types.

36
Q

When does the H-W equilibrium breakdown?

A

If there are other important factors operating such as selection or migration.

37
Q

Give the equations for H-W equilibrium.
Then describe how they relate to a population with two alleles A and a segregating at a particular locus.

A

p + q = 1

(alleles A and a)

p^2 + 2pq + q^2 = 1

(genotypes = AA, Aa, aa)

38
Q

What is ACHOO syndrome?

A

Autosomal dominant compelling helio-opthalmic outburst is characterised by the uncontrollable sneezing response (or prickling sensation in the nose) to sudden exposure to bright light.

Exact genetic mechanism is unknown but from pedigree analysis = autosomal dominant.

Pedigree analysis is a method used in genetics to study the inheritance patterns of traits within a family across multiple generations. By analysing a pedigree, which is a family tree diagram showing relationships among family members and their phenotypes (observable traits) for a specific genetic trait, geneticists can deduce information about how the trait is inherited and whether it’s likely to appear in future generations.

39
Q

What kind of trait is red-green colour vision deficiency?

A

Sex-linked (X-chromosome).

40
Q

How is red-green colour vision deficiency scored?

A

Using Ishihara coloured test.

14% of males and 2% of females.

41
Q

How many phenotypic classes are there for blood group?

A

4 - A, B, AB, O.

42
Q

How are the four blood groups distinguished?

A

According to immunological properties of both red blood cells (erythrocytes) and the serum.
All red cells possess one, both or neither antigens A and B.
Serum contains one/both/neither antibodies anti-A and anti-B

43
Q

How are the antigens and antibodies combined?

A

In a manner that any individual lacks the antibody which would agglutinate their own blood but carries the complementary antibody.

44
Q

List blood groups and their genotypes.

A

O - ii
A - i^Ai or i^Ai^A
B - i^Bi or i^Bi^B
AB - I^Ai^B

45
Q

What would a blood group test involve?

A
  1. Pricking a surface sterilised finger with a
    sterile lance device.
  2. Applying 2 drops of blood to a
    microscope slide marked at 2 places (anti-
    A and anti-B).
  3. Adding 1 drop of the appropriate anti-
    serum and mixing with a toothpick.
  4. Observing whether agglutination occurs.
46
Q

Why did we not do this?

A

Blood group testing prevents health (bruises, infection, pain, fainting) and ethical risks (family disputes and invasion of genetic privacy).

47
Q

What is tongue rolling?

A

The ability to form a U shape with tongue, dominant.

48
Q

What is Hitch-Hiker’s thumb?

A

Ability to bend thumb joint back at 90 degrees, dominant.

49
Q

What is mid-digital hair?

A

Presence of hair on top surface of middle bone of fingers, dominant.

Genetics (10 decks)

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