Beruflich Dokumente
Kultur Dokumente
Thanks to Prof Wu Jinlu, Prof Cynthia He Yingxin and Prof Chew Fook Tim for their
lectures and slides, of which these notes are based on.
Miscellaneous
Definition list
1. Centromere
a. It is the DNA part of the chromatids that is below the kinetochore
proteins, linking sister chromatids
2. Kinetochore
a. It is the protein found at the centromere, where spindle fibres attach
during cell division
b. It has an inner plate that interacts with the centromere, and an
outer plate which the positive end of the spindle fibre attaches
3. Centrosome
a. It is an organelle in animal cells that act as the microtubuleorganising center
b. Made from 2 centrioles
4. Centriole
a. A structure made from 9 sets of triplet microtubules, which is made
from tubulin
5. Chromosome
a. It is a structure, made from DNA and proteins, containing genetic
material of an organism
b. A pair of non-sister chromosomes are homologous, being nearly
identical in shape and size
c. Can be either chromatid or chromatin
i. Usually a pair of sister chromatids is called a chromosome
during division.
6. Chromatin
a. It is a chromosome during interphase, where it is loosely packed to
allow for transcription.
7. Chromatids
a. It is a chromatin that has replicated. It has 2 forms: thread-like
chromatids after S phase, and condensed chromatids after prophase
b. It is used in the context of sister or non-sister chromatids of a
chromosome during division
8. Tetrad/ bivalent
a. Both refer to the pair of homologous chromosomes associating with
each other.
b. However, tetrad can also mean when the 4 chromatids are clearly
visible at diplotene and diakinesis
9. Horizontal gene transfer
a. When genetic material is transferred from one organism to another
that is not its offspring
10.Conjugation
a. It is the transfer of genetic material between bacterial through
direct cell to cell contact
11.Conjugants
a. Cells that are undergoing conjugation, the DNA donor and recipient
12.Exconjugants
a. Any two cells that have previously mated
13.Transconjugants
a. The recombinant descendants of recipient exconjugants
14.Nucleotide
a. The building block of DNA, consisting of a pentose sugar, a
nitrogenous base and a phosphate group
15.Nucleosome
a. A subunit of chromatin, consisting of a histone octamer with DNA
wrapped around it.
16.Gene
a. Controls the phenotype of an organism
17.Allele
a. Alternate forms of a gene and is inherited from parents
18.Locus
a. The site of a specific gene or DNA sequence on a chromosome
19.Genotype
a. An organisms collection of genes and their combination of alleles
20.Phenotype
a. Physical expression of a genotype that may or may not be visible
i. Outward appearance
ii. Proteins
iii. Behaviours
21.Homozygote
a. A diploid organism having two identical alleles at the target locus on
homologous chromosomes
22.Heterozygote
a. A diploid organism having different alleles at the target locus on
homologous chromosomes
23.Hemizygote
a. A diploid organism that has only one allele of a gene
i. Such as genes on the X-chromosome for males
24.Dominant allele
a. An allele that is expressed when at least one copy is present
25.Recessive allele
a. An alleles whose expression is masked by a dominant allele
26.Autosome
a. A non-sex determining chromosome
27.Sex chromosome
a. A chromosome containing genes that specify sex
28.Penetrance
a. It is the proportion of a genotype that expresses a trait, even mildly
29.Expressivity
a. It is the intensity of the phenotype of individuals of a particular
genotype, out of those already affected by that genotype
30.Pleiotropy
a. A gene that causes multiple effects
b. Not all effects need be expressed in an individual
31.Multiple alleles
a. When a given gene has 2 or more alleles that exist in the gene pool
e. During Anaphase
i. The kinetochore no longer joins the sister chromatids
together at the centromere
Each chromatid is now only linked to one pole
ii. Anaphase A and B occurs concurrently, the centromeres
move apart while the microtubules shorten by degradation
Anaphase A is the shortening of microtubules at the +
end (the end furthest from the centrosome)
Either by ATP-driven motor protein causing both
depolymerisation and chromosome movement
Or the microtubule disassembly drives chromosome
movement
iii. Anaphase B is the growth of polar microtubules towards each
other, pushing each other when the polar microtubules meet
in the middle
f. During Telophase
i. Chromatids reach respective poles and decondense into
chromatin
ii. Nuclear membrane reforms around the chromatin, forming
two separate nuclei
iii. Cytokinesis occurs concurrently
Cleavage furrow forms and splits the parent cell into
two
3. Prophase I of meiosis has several sub-stages
a. Leptotene is the condensation of chromatin threads to form
chromosomes
b. Zygotene is when homologous chromosomes pair up to form
bivalents, with a synaptonemal complex forming
i. Homolog recognition occurs with a pairing centre, located at
sister chromatids at either the telomere or centromere.
Proteins in the nuclear membrane recognise and bind
to the highly repeated sequence.
The protein then moves around the membrane until it
contacts the other homologous pair
A synaptonemal complex then forms between the
bivalent
c. Pachytene is the crossing over between non-sister chromatids,
forming a chiasma, with the synaptonemal complex fully formed
i. Synaptonemal complex causes the crossing over
d. Diplotene is the start of dissociation of the synaptonemal complex,
but chromosomes are still linked by the chiasma
e. Diaknesis is when the dissociation of the synaptonemal complex is
finished, and the dissolution of the nuclear membrane
i. After Diaknesis, the bivalent is still linked by the chiasma, and
move together to the metaphase plate, arranging themselves
with independent assortment.
4. Prometaphase I occurs similarly to mitosis. Centrosomes move, 3 types of
spindle fibre forms, attachment to kinetochore occurs
5. The rest of meiosis differs from mitosis
a. During metaphase I
i. Pairs of sister chromatids are aligned along the metaphase
plate in a double row instead of a single row
Bacterial diversity
1. Bacterial usually reproduce asexually by binary fission, thus horizontal
gene transfer is needed to encourage genetic diversity
a. Conjugation involves direct cell to cell contact
b. Transduction involves viruses
c. Transformation involves uptake from the environment
2. During conjugation between a F + cell and a F- cell
a. Cells that have conjugative plasmids (that contain the fertility
factor) contain the genes required for conjugation
i. Such as for pilin protein needed for sex pilus formation
+
b. F cells form sex pili that initiates genetic transfer on contact with a
recipient cell
i. They are hollow structures on the cell surface
c. On contact, relaxosome, a protein complex, separates DNA strands
in the conjugative plasmid
i. Contains relaxase that cuts one strand of the plasmid DNA at
the origin of transfer
ii. This produces a strand called T-DNA which gets transferred
d. T-DNA-relaxase complex is recognised by the coupling factor which
moves it into the exporter
i. Both the coupling factor and exporter are part of the sex
pilus, and are encoded by the conjugation plasmid
e. T-DNA-relaxase complex then moves through the mating channel
into the recipient cell
i. The other conjugation plasmid DNA strand remains in the
donor cells
f. Relaxase then circularised the T-DNA in the recipient cell
g. DNA replication processes in each cell then replicates the single
stranded DNA into a F plasmid
i. Both cells are now F+
h. This process is similar even if the cell is F
i. F cells have chromosomal genes in their F plasmid
3. During conjugation between a Hfr cell and a F - cell
a. When a F+ cell has its F plasmid integrate into the bacterial
chromosome, it becomes a Hfr strain
6.
7.
8.
9.
Molecular Genetics
Structure of DNA and RNA
1. Genetic material has several parts that meets its role
a. It contains the information necessary to code for an entire organism
b. It is hereditable and is passed from parents to offspring
c. It is replicable, to pass from within, and between organisms
(hereditary)
d. It is variable, to be able to react to changes
i. To account for the phenotypic variation seen between species
2. The genetic material was first identified to be in the chromosome, which
consists of both proteins and DNA
a. While DNA had only 4 nucleotides, ATCG, proteins have 20 different
amino acids
b. There was more protein by weight that DNA in chromosomes
c. Variations in proteins were identified, that they are responsible for
different functions
3. Several experiments showed that the genetic material was DNA instead of
proteins
a. Frederick Griffith experiments with Streptococcus pneumoniae
i. Showed that genetic material survived heat treatment
ii. The bacterial cell type could change through the process of
transformation
Recessive, non-lethal type with heat-killed dominant,
lethal type, killed the lab rat
b. Aver, MacLeod and McCarty experiments
i. Showed that the genetic material was DNA, and not RNA or
proteins
ii. Added DNA of dominant phenotype of recessive cell type and
grew with various enzymes
None = grew
a. To show the extract contained genetic material
DNase = no growth
a. To show DNA was responsible
RNase = grew
a. To show RNA was not responsible
Protease = grew
a. To show proteins was not responsible
c. Hershey and Chase experiment with Bacteriophage T2
i. Showed that genetic material was DNA not protein
Bacteriophage T2 only has DNA and protein
ii. Either viral proteins or DNA were radioactively labelled with P
or S
To identify if the bacterial cell take up DNA or proteins
iii. Radioactivity of solution not taken up by bacterial showed
more S than P present
Conclude that bacterial cells take up DNA rather than
proteins.
Thus DNA is the genetic material
4. Other research shows that RNA can also function as a genetic material
5.
6.
7.
8.
9.
A core enzyme of
2 '
A sigma factor of
a. Transcription
i. Rate of assembly of RNA polymerase complex
b. RNA processing
i. Effectiveness of modification
ii. Alternative RNA splicing
c. Exporting
i. Efficiency of export proteins
d. Translation
i. Rate of ribosome complex assembly
ii. Structure of mRNA
iii. Rate of degradation of mRNA
e. Protein modification
i. Molecular chaperones to help protein folding
ii. Covalent modification needed for proper protein folding
Glycosylation
Phosphorylation
Acetylation
iii. Cofactors and other protein subunits
iv. Degradation by proteasome, especially for incorrectly folded
proteins
Population genetics
Inheritance types
1. Factors influencing phenotypic ratios
a. Complete or incomplete or co-dominance or sex-influenced or sexlimited
i. Partial dominance leads to intermediate phenotypes
ii. Sex-influenced dominance will cause intermediate to have
different phenotypes based on gender
iii. Sex-limited will only have the phenotype expressed in one
gender
b. Autosomal or sex-linked
i. More males are affected when sex-linked
c. Monohybrid or dihybrid
d. Lethal or non-lethal
2. Expected phenotypic ratios in F2, with opposite homozygous parents
(heterozygous F1)
a. Autosomal complete dominance monohybrid cross
i. 3 dominant: 1 recessive
b. Autosomal incomplete dominance monohybrid cross
i. 1 dominant: 2 intermediate: 1 recessive
c. Autosomal complete dominance dihybrid cross
i. 9 dominant-dominant: 3 dominant-recessive: 3 recessivedominant : 1 recessive-recessive
d. X-linked dominant
i. Male:
ii. Female:
e. X-linked recessive
i. Male:
ii. Female
f. Y-linked
g. Recessive epistasis of autosomal complete dominance dihybrid
cross
i. 9 dominant-dominant: 3 dominant-recessive : 4 recessive-_
Because recessive-dominant looks like recessiverecessive
h. Dominant epistasis of autosomal complete dominance dihybrid
cross
i. 12 dominant-_: 3 recessive-dominant : 1 recessive-recessive
Because dominant-recessive looks like dominantdominant
i. Complementary loci of autosomal complete dominance dihybrid
cross
i. 9 dominant-dominant : 7 recessive
Because any recessive will give the same phenotype
j. Duplicate dominant genes of complete dominance dihybrid cross
i. 15 dominant : 1 recessive-recessive
Because any dominant will give the same phenotype
k. Duplicate genes with cumulative effect
i. 9 dominant-dominant : 6 dominant + recessive: 1 recessiverecessive
l. Dominant and recessive interaction
i. 13 dominant-_ : 3 recessive-dominant
Because dominant-_ looks like recessive-recessive
3. Reading pedigree
a. Determining type of inheritance
i. Autosomal dominant diseases
Affects both males and females equally
Does not skip generations
ii. Autosomal recessive diseases
Affects both males and females equally
Does skip generations
iii. X-linked dominant
More affected females than males
May be lethal in hemizygous males, causing
decreased male count
Mendelian Genetics
1. There are several reasons why Mendel used the pea plant for this
experiments
a. It has well defined characteristics
b. Pure-bred varieties are available
c. The flowers have male and females parts, allowing for selffertilisation
d. Both self and cross fertilisation are possible
e. Relatively short life cycle
f. Large number of offspring produced from each mating
2. Mendels law of segregation states that the gamete only contains one
allele of a gene
a. Thus both alleles of a parents gene are not inherited together in
one gamete
3. Mendels law of independent assortment states that each allele in the
parental pair, will combine randomly with either allele in the other
parental pair, when forming the offspring
4. Partial dominance occurs when each genotype has a distinguishable
phenotype, with the heterozygote having an intermediate trait between
the two homozygotes extremes
5. When considering
n
a.
b.
3n
c.
numbers of loci
complete dominance
i. Else there will be
incomplete dominance
6. Testcross is used to identify the genotype of an organism, whether it is
heterozygous or homozygous for the gene
a. The organism is mated with a homozygous recessive tester stock
b. If only one offspring phenotype is observed, the original organism is
homozygous.
7. Reciprocal cross is used to determine if the gene is sex-linked
a. A homozygous dominant male is mated with a homozygous
recessive female and vice-versa
b. Autosomal genes will have equal results, while sex-linked genes will
have different ones
8. Males are more affected by recessive X-chromosome diseases, as they are
hemizygous
9. There is a criss-crossing of recessive X-chromosome alleles
a. Affected mothers will definitely give affected sons
b. Affected fathers will definitely give carrier daughters
i. Daughters may be affected if mother is also carrier or
affected
10.Barr bodies are found in female cells, as one X-chromosome is inactivated
a. One of the two X chromosomes in female cells is in the
heterochromatin state
b. Usually females cells will only have one Barr body, but the number
can differ due to aneuploidy
11.Autosomal genes can be sex-influenced, with the heterozygotes having
different phenotypes based on gender
12.Autosomal genes can also be sex-limited, where only one gender gets
affected
13.Having the genotype does not necessarily mean the individual is affected
a. Penetrance and expressivity measures this
b. Pleiotropy also leads to not all effects being caused
14.Multiple Alleles will cause an increase in the number of genotypes
a. Number of genotypes =
n(n+1)
, where
2
is the number of
alleles
15.Epistasis occurs when the genotype at one locus suppresses the
expression of the alleles of another locus
16.Recessive epistasis requires for a homozygous recessive genotype to mask
the other gene
a. Loci for gene A has recessive epistasis over loci for gene B
b. Caused by the loss of production of intermediate, masking the
effect of the other gene
i. Like ability for coat to have colour
c. Caused by leaky allele, where two recessive alleles gives rise to an
effect similar to a dominant allele
17.Dominant epistasis requires only one copy of the allele at the epistatic loci
a. The expression of the dominant allele masks the expression of the
other gene
i. The dominant allele causes the phenotype regardless of the
allelic conditions of the other locus
b. Cause by the dominant allele degrading the precursor or product of
the other gene
18.Complementary loci (Duplicate recessive gene) is when the recessive
alleles for both genes give the same phenotype
a. Like colourness and purple vs white
b. Caused by the pathway having a colourless precursor and colourless
intermediate
c. Caused by needing both products to form a functional dimer
19.Duplicate dominant gene is when the dominant alleles for both genes give
the same phenotype
a. Both genes lead to the same final product, and phenotype is
independent on the relative quantity of final produce produced
Non-Mendelian Genetics
1. Maternal inheritance is non-Mendelian because the mitochondrial DNA can
only be passed down from mother to offsprings
a. Mitochondrial DNA undergoes high rates of mutation
i. Due to exposure to free radicals from respiration
ii. Due to no DNA repair during replication
iii. Due to its numerous copies in each mitochondria
b. Thus can be used for comparison between species that diverged
only a short time ago
2. Linked genes are non-Mendelian because they do not obey Mendels Law
of Segregation
a. The genes tend to be inherited together, affecting the offspring
genotypic ratio
i. Parental genotype will be greater than recombinant genotype
0 0.5
ii. 1 cM
0.01 (
value)
They are not equal when the real distance between loci
is great
There will be less recombinant frequency than
expected, as even numbers of chiasmata formation
between the loci produces a parental gamete
iii. Since the Mendelian ratio is 1:1:1:1, which means 50% parent
and 50% recombinant
b. A value of 0.1 would imply that crossing over to form recombinant
gametes occurs once every 10 times
c. A value of 0.5 would imply that recombinant gametes are form half
the time meaning that the gene are either physically or genetically
unlinked
5. For linked genes, a heterozygote (AaBb) can have different forms of the
same genotype
a. Depends on the parents genotype
i. AABB x aabb
ii. AAbb x aaBB
b. Trans arrangement is when the mutant alleles are carried by both
chromosomes
i. Ab + aB
c. Cis arrangement is when one chromosome carries the wild-type
allele, and the other carries the mutant allele
i. AB + ab
6. Linkage analysis can be done to associate a certain form of a marker with
the disease allele of a gene
a. Closely linked markers with the disease allele will cosegregate
Population Genetics
1. A population has a large group of sexually-reproducing interbreeding
individuals with a common gene pool
2. Hardy-Weinberg equilibrium is achieved when a population has no changes
in genotype frequency, at a specific loci, over generations.
a. Actual numbers of individuals with the genotype may change, but
the overall genotype frequency remains constant
b. When
a
population
is
in
Hardy-Weinberg
equilibrium,
p+q=1
p+q+ r=1
p2+ q2 +r 2 +2 pq+2 pr +2 qr =1
c. The values of the genotype frequency, when there is HardyWeinberg equilibrium, is not fixed
i. When conditions change from ABC to ABD, and back to ABC,
the equilibrium genotype frequency at the first ABC is not
the same as during the second ABC
3. Hardy-Weinberg equilibrium is obtained when certain conditions are
satisfied
a. There must be a large population size, to minimise the effects of
genetics drift
i. Since mating and survival is random, the genotype of a small
population will fluctuate greatly
Fixation occurs when one allele is lost from the gene
pool
This is more likely to occur in small populations
b. There needs to be random mating
i. Non-random mating leads to increases in the frequency of
homozygotes in the sub-population
pn= p0 ( 1 )
q e = p e
is the rate of mutation of
q , and
whose frequency is
q e=
, pe =
+
+
1s
iii. A fitness of 0.5 means that for every one offspring produced
by the less fit genotype, 2 offspring are produced by the
fittest genotype
Thus the population has more of the fittest genotype
b. To find the allele frequency when it is selected against
i. Assume that the population is in Hardy-Weinberg equilibrium,
such that the observed number are equal to the expected
numbers
ii. Calculate the current allele frequency of all alleles
iii. Calculate the gametic contribution of each genotype
Genotype frequency times fitness
iv. Derive the allele frequency over one generation
q1 =
s 1 p e=s 2 q e
ii.
pe =
s2
s
, qe = 1
s 1+ s 2
s 1+ s 2
1
Number of organisms with A 1 A1 + ( Number of organisms with A1 A 2)
2
p=
Totalnumber of organisms
b. Calculate the frequency of the second allele ( A 2 )
i.
1
Number of organisms with A2 A 2 + ( Number of organisms with A 1 A 2)
2
q=
Total number of organisms
c. Calculate the expected frequency of each
population is in Hardy-Weinberg equilibrium
i.
A 1 A 1= p , A 1 A2=2 pq , A 2 A 2=q
genotype
if
the
numbers
for
genotype
A1 A1
is
iii. Perform
-test
iv. Compare
Degree
freedom
is
p+q=1
2
1
( Allele frequency females )+ ( Allele frequency males)
3
3
p1 p 2
a. Z-score =
p 1 ( 1p 1 ) p2 ( 1 p2 )
+
n12
n22