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Summary molecular biology Practical Biological Chemistry €6,49
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  3. Wageningen University (WUR)
  4.  
  5. Practicum Biologische Chemie (BIC10306)

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Summary molecular biology Practical Biological Chemistry
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A summary of the molecule biology part of Practical Biological Chemistry. Chapters: H1: 1.1 & 1.2 (general) H7: 7.1, 7.2, 7.4, 7.5; DNA structure H8: 8.1, 8.3, 8.4; RNA transcription and processing H9: 9.1, 9.2, 9.3, 9.4 (general concept); protein synthesis H10: 10.1, 10.2, 10.3; Gene isolat...

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  • 26 april 2021
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Introduction to genetic analysis
Summary wur for molecular biology

H1: 1.1 & 1.2 (general)
H7: 7.1, 7.2, 7.4, 7.5; DNA structure
H8: 8.1, 8.3, 8.4; RNA transcription and processing
H9: 9.1, 9.2, 9.3, 9.4 (general concept); protein synthesis
H10: 10.1, 10.2, 10.3; Gene isolation and manipulation
H12: 12.1 tot lessons from the yeast GAL system, 12.2; Regulation of transcription in eukaryotes
H14: 14.3, 14.4; Bioinformatics
H15: H15.1; Molecular consequences of point mutations
H16: H16.1, H16.3, H16.4; Transposable elements


Chapter 1

In the 1800s, inheritance was thought of as the blending theory, it works like mixing fluids. With that,
all individuals would have had the same average values of traits. Mendel proposed that factors
behave as particles rather than fluids. These particles are nowadays known as genes. Each individual
plant has two copies of genes in cells of the body (somatic cells) and one copy in the sperm
(gametes). He also proposed that genes can vary on alleles, where one allele can be dominant.
Genetics is the study of inheritance. Genes are located on chromosomes and Fisher discovered that
traits can be controlled by multiple genes. Genes are made of DNA, where genetic information can
be stored in the bases (A, C, T and G). Bonding is based on complementary shapes and charges of the
bases. Genes have regulatory elements that control gene expression. The central dogma is the flow
of DNA to RNA to protein (transcription and translation). DNA can also be replicated. Translation
happens via codons, a set of three nucleotides in the mRNA. A model organism is a species used for
analysation with the assumption that the outcome of the analysation is true for other species. A
model organism must be small (easy to maintain and inexpensive), have a short generation time,
have a small genome and be easy to cross. Genetic strains (colours of plants etc) enable scientists to
study how genes influence physiology, development and disease. DNA polymerase can make a copy
of a strand, nucleases can cut DNA molecules and ligases can join two DNA molecules together
(methods to perform enzymatic machinery). Scientists can also clone (making copies) DNA. This DNA
is often inserted in a host cell (transformation). The recipient species become genetically modified
(GMO). Scientists can also hybridize DNA molecules to one another and they can determine the exact
sequence of bases (DNA sequencing). Lastly, scientists have created tools to analyse an entire
genome, genomics.

Chapter 7

Griffith discovered that the genotype and phenotype can be changed by mixing it with a different,
heat-killed bacterial strain. He discovered a process of transformation (chapter 10). It is now known
that fragments of transforming DNA replace their counterparts on chromosomes. It was the first
evidence that genes are composed of DNA.
Radioisotopes are unstable isotopes of an element that emit radiation to transform to a more stable
form. Adding this indicated the hereditary function of DNA.
DNA must have three properties; accurate replication is crucial, it must have informational content
and it must be able to change on rare occasion (mutations). DNA is composed of three components,
phosphate, deoxyribose and four nitrogen bases (adenine, guanine, thymine and cytosine). A and G
are part of the purines, C and T are part of the pyrimides. The chemical subunits of DNA are called

, nucleotides or deoxynucleotides. The total amount of A and G always equals the amount of C and T
and the amount of A always equals T and vice versa. The amount of A + T is not always equal to C+G.
DNA is a long and skinny, two stranded helix. G only pairs with C and A only pairs with T. These are
called complementary bases. The two strands are held together by hydrogen bonds. The backbone is
formed by phosphate and deoxyribose sugar, linked by phosphodiester linkages. In a helix, the two
backbones are antiparallel (5’ to 3’ and the other from 3’ to 5’). A and T have two hydrogen bonds, C
and G have three hydrogen bonds. When phosphates and sugars are far apart, a major groove exist.
When they are close together, a minor groove exist.
The genetic code is written in the nucleotides and the copying mechanism of DNA is
semiconservative.
The replisome contains proteins for unwinding the double strand; helicases and topoisomerases.
Helicases disrupt hydrogen bonds. Unwound DNA is stabilized by single strand DNA-binding (SSB)
proteins. These prevent the duplex from reforming. Topoisomerases (like gyrase) remove supercoils
and turns in unwound DNA. Assembly of the replisome begins at the origin of replication on a
chromosome. DnaA binds to DnaA boxes and regulates unwinding. Then, helicases bind and slide in
5’ to 3’ direction. In E. Coli, five types of DNA polymerases are found. DNA polymerase I functions as
catalyser for chain growth, removal of mismatched nucleotides and degradation of single strands.
Growth occurs in 5’ to 3’ direction. DNA polymerase III catalyses DNA synthesis at the replication
fork. Synthesis must be initiated by a primer (short chain of nucleotides), synthesized by a
primosome of which a central component is primase (an RNA polymerase). The leading strand can
be synthesized smoothly, the lagging strand can only be synthesized in short fragments, Okazaki
fragments. The overall process is thus semidiscontinuous. DNA polymerase I removes the primers
and ligase catalyses the formation of phosphodiester bonds and joins the strands together. Both DNA
polymerase I and III have proofreading activities, they can remove mismatched bases. Primase lacks
proofreading activity. DNA polymerase III is part of a much larger complex; DNA polymerase III
holoenzyme. This is part of the replisome which coordinates synthesis. Attachment of DNA
polymerase III is maintained by the beta clamp (sliding clamp) and the clamp loader. The beta clamp
transforms DNA polymerase III from a distributive enzyme to a processive enzyme. Primase doesn’t
touch the clamp protein and is a distributive enzyme.
Eukaryotic chromosomes have multiple origins of replications and replication proceeds in both
directions. Synthesis only takes place in the S phase of the cell cycle. The origin of replication binds to
sequences in the origins. This recruits Cdc6 and they load a complex together of Cdt1 and helicase.
Cdc6 and Cdt1 are only available in certain phases in the cell cycle. ORCs binds to other protein
complexes on chromosomes, because they can’t bind to the replisome directly. When the last primer
of the lagging strand is removed, sequences lack the final nucleotides, the telomers. Telomerase
adds the repeated sequences back to the chromosome ends. Telomerase is a protein complex with a
special type of DNA polymerase, known as reverse transcriptase. This sequence is added to the 3’
end. Telomeres preserve chromosomal integrity by forming a protein structure with WRN, TRF1 and
TRF2, called a telomeric loop. This structure hides chromosome ends for repair machinery. Somatic
cells produce very little or no telomerase. Telomeres are associated with aging and cancer.


Chapter 8

An intermediate, RNA, carries DNA from the nucleus to the cytoplasm. RNA has a high rate of
turnover within cells. RNA is synthesized in the nucleus and then moves to the cytoplasm for
synthesizing proteins. RNA has ribose instead of deoxyribose in DNA. RNA contains uracil instead of
thymine in DNA. Uracil can base pair with both adenine and guanine. RNA can therefore form
intricate structures. RNA is usually single-stranded, is more flexible and can form a greater variety of

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