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Summary of Cell Physiology and Genetics, BIC20306, wur
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A summary of the two books 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 geneticssummary
CASE 1, SICKLE CELL DISEASE
Genetics
All living things are made of cells. The parent organism hands down information specifying the
characteristics that the offspring shall have; heredity. All living cells store their hereditary information
in the form of DNA, made of the four bases A, C, T and G. Each nucleotide is made of a base, a
phosphate group and a sugar. DNA replication can occur, where new strands are formed using a
template strand (base-pairing). DNA can express
itself using the mechanisms of transcription,
where RNA is made, and translation. After
transcription, mRNA is made, which can serve as
the base for the production of proteins. Proteins
are long, unbranched polymer chains. Proteins
are made of amino acids. Each of the protein
molecules is a polypeptide, created by joining its
amino acids in a particular sequence. Proteins can
act as enzymes to catalyse reactions or to break
covalent bonds.
Transfer RNAs can read the codons (the genetic code) of mRNA and can find the anticodon. This is
the amino acid that binds in the protein. This happens in the ribosome.
A gene is a piece of a DNA segment. The genome of the cell is thus the totality of its genetic
information. All cells require ATP as the carrier of free energy to drive a number of chemical
reactions. Cells are enclosed by a plasma membrane, which serves as a selective barrier. This barrier
is amphiphilic, both hydrophobic as hydrophilic.
Eukaryotes keep their DNA in the nucleus, prokaryotes have no nuclear compartment. Prokaryotes
can be divided into bacteria and archaea. The nucleus is surrounded by a nuclear envelope (double
membrane layer) and eukaryotic cells have a cytoskeleton. Eukaryotic cells also have mitochondria,
with their own genome. Plants and algae cells have chloroplasts, which also have an own genome.
Fungal cells have mitochondria, but not chloroplasts.
In the storage and copying of genetic information, random accidents and errors occur, called
mutations. Through the cycle of mutations and natural selection, organisms evolve.
A complete DNA sequence can reveal the genes an organism has and the genes the organisms lacks.
Innovation can occur due to: intragenic mutations, gene duplication, DNA segment shuffling and
horizontal transfer (DNA goes from one genome of one cell to that of another). A cell duplicates its
genome each time it divides into two daughter cells. Analysis of this has revealed entire gene
families. Orthologs are genes that derive from the same ancestral gene in the last common ancestor
of two species. Paralogs are related genes within a single genome (result from gene duplication).
Homologs cover genes that are related in both ways described above.
Viruses are small packages of genetic material that have evolved as parasites on the reproductive and
biosynthetic machinery of host cells. They are not living cells itself. They can live as a small piece of
,DNA, called a plasmid, in its host cell. This process is called horizontal gene transfer. Sex is also a
cause of horizontal gene transfer.
Genetics starts with the study of mutants, we either find or make an organism in which a gene is
altered, and then examine the effects. Biochemistry more directly examines the functions of
molecules. To make sense of gene functions, we must study whole organisms. Often, different aspect
of the same model organism (E.coli) are studied.
98.5% of the eukaryotic genome is noncoding DNA, in contrast to 11% in bacteria. The noncoding
DNA can regulate the expression of adjacent genes, it is thus regulatory DNA.
Often, eukaryotes have multicellular complexes. Because this is difficult to investigate, scientists use
a model species, a unicellular eukaryote S.cervisiae. This cell can also undergo meiosis.
Recombinant DNA technology is the ability to manipulate DNA with precision in a test tube or an
organism. This has had dramatic effects on the DNA techniques, for example the development of
cloning. Restriction nucleases can cut the double helix at specific sites defined by the local nucleotide
sequence, thereby cleaving it into fragments of strictly defined sizes. Different bacterial species
create different restriction nucleases. The same types of gel-electrophoresis (using agarose), useful
for investigating proteins, can be used for DNA molecules. There is no need to add a negative charge,
because each nucleotide already carries a negative charge. The bands can be made visible using
ethidium bromide as staining.
DNA cloning can be defined in two ways. It is the making of identical copies of a DNA molecule and
the isolation of a particular stretch of DNA from the cell’s genome. One of the simplest methods is
inserting a DNA fragment into the purified DNA genome of a self-replicating element (plasmid
vectors). These plasmid circles are first cut using restriction enzymes, to make linear fragments. DNA
ligase can fuse the fragments and the DNA fragment. The cells divided and clones are made. The
collection of cloned plasmid molecules is known as the DNA library. The resulting collection, the
genomic library, will represent the entire genome of an organism.
mRNA can also be cloned. This is done by extracting the mRNA and then making a DNA copy of it, the
cDNA using reverse transcriptase. This can be used for vectors, giving a cDNA clone and a cDNA
library. A distinct cDNA library is obtained for each type of cell.
The PCR method can detect a single DNA molecule in a sample if at least part of the sequence is
known. Trace amount of RNA can be detected by first converting them to DNA. PCR makes it possible
to create a DNA fingerprint of an individual. PCR allows DNA cloning to be performed directly using
DNA polymerase and primers.
The dideoxy or Sanger sequencing method is widely used to determine the nucleotide sequence of
any purified DNA fragment. This method uses DNA polymerase to make copies of the fragment.
These copies lack the 3’-hydroxyl group, which blocks further elongation.
The process of genome annotation attempts to mark out all genes in a genome and ascribe a role to
each. The first step is to transform the entire genome into proteins. Each double DNA strand has six
open reading frames; six ways of reading the nucleotides. The ORFs are checked using a database
(comparative genomics). If matches are found, it is likely that the ORF codes for a functional protein.
By sequencing total RNA, it is possible to investigate possible alternative splicing places. RNA-seq also
identifies noncoding RNAs. Working backwards from the phenotype, the appearance or behaviour of
an individual, one can deduct its genotype.
A type of mutations is insertional mutagenesis, where exogenous DNA inserted in the genome can
create mutations (such as radiation). One a collection of mutants in a model organism has been
produced, men must perform a genetic screen to find the altered phenotype of interest. Most
, mutations are lethal, so the function of these genes are studied with conditional mutations. These
mutations only demonstrate abnormal functions under restrictive conditions (such as temperature
sensitivity). Gene mutations are generally classed as loss or gain of function. A dominant mutation is
one that still causes the mutant phenotype when there is only one copy. A recessive mutation needs
two copies. Alleles are alternative forms of the same gene. A complementation test can be used to
ascertain whether a mutation falls in the same gene or in a different gene (mating is used). Epistasis
analysis is the analysis where the order in which the genes act is discovered. A synthetic phenotype
indicates that two genes act in two different parallel pathways.
When two sequence variants coexist in a population and are both common, these variants are called
polymorphisms. The majority of variants are due to the substitution of a single nucleotide, single-
nucleotide polymorphism (SNPs). Insertions, indels, or deletions can also be a cause. The variants
tend to travel in groups called haplotype blocks.
Single gene or monogenic disorders are often referred to as Mendelian, because their pattern of
inheritance is easy to follow. Multigenic conditions also occur (diabetes for
example), where environmental factors play a role. De novo mutations arouse
spontaneously in the germ-line cells of one or the other parent.
Reverse genetics is the procedure where a scientists takes a gene and mutates it.
This can be done to follow the effects of a mutations. This is also called genome
editing or genome engineering. One way of editing is using gene knockouts,
where the genes are deleted. Deletion can also be done in certain tissues.
Another way of engineering is using gene replacing. Subtle changes can also be
performed. This can be the changing of a single amino acids. Transgenic
organisms are animals or plants which have been genetically engineered.
Transgenes are the modified genes. This is often done with mice (see image).
RNA interference can be used as an alternative approach. Double-stranded RNA,
which matches the nucleotide sequence of the gene to be inactivated, is brought
into the target RNA. This reduces the expression of the mechanisms.
Key insights into gene function can be obtained by simply observing when and where a gene is
expressed. This can be done by placing a reporter gene into cells. The green fluorescent protein (GFP)
is an example of such a protein.
Quantitative RT-PCR begins with the total population of RNA molecules. This measurement can track
the progress of the reaction and deduce the concentration of mRNA amplified.
With the DNA microarray, the RNAs produced by cells and tissues can be analysed. Probes are used.
Using cluster analysis, one can identify a set of genes that are coordinately regulated.
Ribosome profiling can be used to follow the translation of a mRNA strand.
Molecular biology
Each chromosome consists of a single, linear DNA molecule along with proteins that fold and turn the
DNA into a more compact structure. Bacteria lack the nuclear compartment and have circular DNA.
Each human cell contains two copies of a chromosome, one from the mother and one from the
father. The pair is called the homologues chromosomes (homologs). The only nonhomologous pairs
are the sex chromosomes. The chromosomes can be distinguished in the early stage of mitosis using
stains. The display of the chromosomes is called a karyotype. Chromosomes carry genes, which are
defined as a segment of DNA that contains the instructions for making a particular protein. Only 1.5%
of the human genome codes for proteins. Half of the chromosomal DNA is made of mobile elements,
transposable elements. RNA consists of exons, the coding sequencing, and introns, the non-coding
sequences. Each gene also consist of regulatory DNA sequences, which are ensuring that the gene is
turned on or off at the proper time.
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