College aantekeningen
Lecture notes Cell Physiology and Genetics, BIC20306, wur
Lecture notes of all lectures of the course Cell Physiology and Genetics, given in the second year of mutiple bachelors at Wageningen University.
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Cell Physiology and Genetics lecture notesGenetics
Genetics can be subdivided into different topics. These topics
are shown in the image on the left.
The genetic information is in our DNA, and can be found in
chromosomes. The genes are the carriers of the genetic
information. The promotor of the gene helps during the
transcription (docking station).
The RNA consists of exons and introns, and only the exons are
used. After intron splicing, the mRNA has been made which can
be used for translation. During translation, proteins can be
made using amino acids.
DNA is prone to changes, due to mutations and replication
errors.
Variations
on genes are called alleles (one gene can have a
different variation of a certain trait than another
gene). This single base difference might result in
a different function or expression.
Genes are considered as the unit of inheritance.
Different forms exist in populations (DNA
polymorphisms and alleles). One gene has an
open reading frame (more in other lectures),
which is the proper order of the sequence for
translation. If you skip one base during
translation, the open reading frame will change. Alternative splicing can also occur, which leads to
different mRNAs. Epigenetic modifications and post-transcriptional modifications can occur too
(more later on).
Genetic information encoded in genes is somehow translated to a certain function. It follows the
steps: DNA->RNA->protein->metabolite->phenotype. The genotype thus encodes for the phenotype,
the characteristics of an individual. A genotype is the connection and combination of alleles in an
individual and the phenotype is its result (in terms of behaviour and looks).
Replication of DNA is needed during cell division (see image
on the left). For the making of proteins (and thus the
phenotype), DNA has to be copied to a RNA molecule.
During the making of proteins, the gene expression is
controlled/regulated. This can occur during the transcription,
translation and after the translation (see image below).
The
transcriptional
control is maybe
the most important control. If the transcription is done
incorrectly, this can have fatal effects. If transcription
can’t take place, life itself is impossible. The control is
,done by a protein with activators, coactivators, basal transcription factors and repressors. The
regulatory elements can bind before the promotor and the RNA polymerase.
RNA is very unstable, because it is single stranded and very vulnerable for degradation. mRNA has a
very low half-life. The half-life is an important aspect to determine how much protein can be
translated from this single mRNA strand.
During translational control, the correct assembly of amino acids is checked. Some amino acids can
have multiple triplets (codons) where they react to. During post-translational control, modifications
after translations are checked. For example, chemical modifications or mistakes during folding of the
protein can occur. Some modifications are reversible, for example when adding a hydroxy-group.
Irreversible modifications can also occur. This is for example when the protein is cleaved.
Genes encode for traits and the allelic variation explains phenotypic variation.
Genes are transmitted through chromosome replication (chromosomes are transferred from a
parent to a child).
Mitosis usually results in
the production of two
genetically identical cells
(somatic cell reproduction).
Meiosis usually results in
the production of four
recombinant haploid cells
(sexual cell reproduction).
So, for meiosis, two
replications need to
happen. Cross-overs or
recombination can occur during the second deviation.
Two homologues chromosomes can exchange genetic
variation. Each embryo can have only one copy of the
chromosome from the mother and only one from the
father.
Mendel is known as the father of modern genetics. He
performed a number of experiments on pea plants and
has discovered the law of segregation, the law of
independent assortment and the law of dominance.
These are also known as the three laws of Mendel.
1. Law of segregation: during gamete formation,
the alleles for each gene segregate
from each other, so that each
gamete carries only one allele for each gene and offspring acquire one allele of
each parent (see image).
2. Law of independent assortment: genes for different traits can segregate
independently during the formation of gametes and the laws of chance govern
which particular characteristics of the parental pairs will occur in each
individual offspring. The principle of independent assortment results from the
independent separation of chromosomes during meiosis.
, 3. Law of dominance: some alleles are dominant while others are recessive; an organism with
at least one dominant allele will display the effect of the dominant allele (think about the
colour of flowers).
Based on information about the genes of parental lines, the outcome of offspring generations can be
predicted. With the squares below (the Punnett squares), the chances of occurrence can be
determined.
For predication, the rule of multiplication can be applied. This is the chance that 2 or more
independent events will occur together. Probability that 2 coins tossed at the same time will land
heads up: ½ * ½ = ¼. Probability if Bb*Bb-> bb is also ½ * ½ = ¼. The rule of addition: is the chance
that an event can occur in 2 or more different ways. It consists of the sum of
the separate possibilities. See the image for this. Explanation: the chance of
getting Bb is ¼. The chance of getting Bb again when creating offspring with
Bb and Bb is ¼ + ¼ = ½.
If you know the genotypes of the parental lines,
you can calculate the probability of certain
characteristics in the offspring.
A summary of the genetic terms can be found on the right.
True Mendalian traits:
• Qualitative phenotypic variations (discrete types, either yellow
or green shape either round or squared etc.)
• All traits are only determined by a single gene
• Each allele is only dominant or recessive
• There is a fixed ratio of segregation in discrete classes (genotypic
and phenotypic), if all the above is true.
• Genes are independent of the genetic background
(environment).
These traits have been chosen by Mendel, but most traits are wrong.
There is a continuous variation, there is genetic and environmental
interaction, complementation (with mutations) and pleiotropy (genes with multiple functions) can
occur. You can also have dominance effects (incomplete dominance and co-dominance), sex-related
effects (X- and Y-chromosomes have also an effect on the ratio of segregation) and gene dosage
effects.
, Heritance trees can be made to determine
diseases in a family. These trees are represented
by the Pedigree symbols and an example can be
seen on the left.
A human karyotype shows the chromosomes.
Autosomes are pairs of homologues
chromosome, one from mum and one from dad.
The karyotype consists of 23 autosomes.
If two affected people have an unaffected child,
it much be a dominant pedigree: H is the
dominant mutant allele and h is the recessive
allele wild type. If two unaffected people have
an affected child, it is a recessive pedigree: F is
the dominant wild type allele and f is the recessive mutant allele type.
Penetrance refers to the proportion of individuals whose phenotype matches their genotype.
Complete penetrance: all individuals of a particular genotype show the phenotype. Incomplete
penetrance: some individuals
fail to express the trait, even
though the carry the right
genotype. Incomplete
penetrance is defined by
discrete categories.
Haplosufficient is when only one
copy of the chromosome is
enough for a gene to be
functional, haploinsufficient is
when this one copy is not
enough.
Traits can also be determined by
sex chromosomes (X and Y). In
females, one of the two X-chromosomes gets silenced. Transmission of an X-linked dominant gene
mutation from an affected male to his offspring is similar to X-linked recessive inheritance; all of his
daughters and none of his sons will inherit the mutation.
Transmission of an X-linked dominant gene mutation from an affected female to her offspring is
similar to autosomal dominant inheritance; each child, regardless of gender, has a 50% chance of
inheriting the mutation.
Traits on the Y-chromosome are only found in males, never in females. The father’s traits are passed
to all sons. Dominance is irrelevant, there is only one copy of the Y-chromosome.
Mitochondria are only inherited from the mother. If a female has a mitochondrial trait, all of her
offspring inherits it. If a male has a mitochondria trait, none of his offspring inherits it. Note that only
one allele is present in each individual, so dominance is not an issue.
During population and evolutionary genetics the frequencies of a specific allele or genotype are
investigated. Population genetics is all about counting alleles and frequencies. The gene pool is all
the different genes and alleles present in a population. In a fixed gene pool, this number can’t
change. A shift in allele frequency can occur due to natural selection and genetic drift. An equilibrium
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