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Summary Genetics
- Vak
- Genetics
- Instelling
- Vrije Universiteit Amsterdam (VU)
A summary of all the lectures given during the course Genetics at the Vrije Universiteit Amsterdam.
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Genetics 2.0 LecturesLecture 1: Chapter 9 DNA/RNA structure
DNA has a central role in the medical sciences:
1. Genetic diseases (faulty genes and or their regulation).
2. Understanding cancer (causes, consequences of genetic changes and
treatments).
3. Diagnostics
4. Genetic therapies, either based on DNA or RNA.
5. Understanding DNA damage and damaging agents.
6. Research in many areas (gene expression, modifying genes and/or their
expression, reporter genes, etc.)
To fulfill its role, genetic material must meet several criteria:
1. Information: it must contain the information necessary to make an entire
organism.
2. Transmission: it must be passed on from parent to offspring.
3. Replication: it must be copied, in order to be passed on from cell to cell and from
parent to offspring.
4. Variation: it is capable of changing to account for the known phenotypic variation
in each species and leads to adaptation and evolution.
In 1869 Johann Friedrich Miescher investigated the chemical composition of the cells
including the nucleus. He isolated an organic acid that was high in phosphorus,
nitrogen, but no sulfur. He called it ‘nuclein’, we now call it DNA (deoxyribonucleic
acid) and he suggested that it could be involved in inheritance.
Through experiments with bacterial pathogens and viruses discoveries providing the
evidence that DNA was responsible for transmitting certain traits were made.
Griffith’s experiment identifying the ‘transforming principle’, gave rats an injection
with rough and smooth virulent, and concluded that DNA is the ‘transforming
principle’ allowing R bacteria to make a smooth coat and allow infection.
Hershey and Chase results bacterio-phages: bacterio-phages are viruses that infect
bacteria, consist of protein and DNA, and inject their hereditary material into
bacteria, as we now know.
Each nucleotide consists of 2’-Deoxyribose (5-carbon sugar), phosphate group and a
nitrogen containing base. There are 4 bases possible, Adenine, Guanine, Thymine,
Cytosine.
A base and a sugar form a nucleoside, adenine + ribose = adenosine and adenine +
deoxyribose = deoxyadenosine.
A base, a sugar and a phosphate group form a nucleotide, adenosine
monophosphate (AMP).
The percentage of adenine is equal to the percentage of thymine, while the
percentage of guanine is equal to the percentage of cytosine. A and T are
complementary bases and C and G are complementary bases.
Rosalind Franklin did a key experiment, she worked in the laboratory of Maurice
Wilkins in Cambridge and used X-ray diffraction to study wet fibers of DNA.
DNA has a double helix shape, with 10 nucleotides per complete 360 degrees turn of
the helix. The double helix shape allows for a major and minor groove.
, Watson-Crick model:
1. Most DNAs consist of two nucleotide strands.
2. The nucleotides are connected by phosphodiester bonds, DNA backbone.
3. The 2 strands run in ‘opposite directions’: antiparallel.
4. Strands are held together by hydrogen bonds between bases.
5. A binds preferentially to T/U and C to G: base pairing.
6. Base ‘stacking’ provides most of the stability of double helix.
7. Most DNA molecules are double-stranded.
8. Nucleotides are covalently linked together by phosphodiester bonds; a
phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of another.
9. Therefore, the strand has directionality/polarity, 5’ to 3’.
10. The phosphates and sugar molecules form the backbone of the nucleic acid
strand, the bases project from the backbone.
DNA can form alternative types of double helices, the DNA double helix can form
different types of secondary structure. The predominant form found in living cells is
B-DNA (right-handed). However, under certain in vitro (and at some places, in vivo)
conditions, A-DNA and Z-DNA double helices can form. DNA structure of
chromosome ends (telomeres).
A-DNA has a right-handed helix, 11 base pairs per turn, occurs under conditions of
low humidity and little evidence suggests that it is biologically important.
Z-DNA has a left-handed helix, 12 base pairs per turn, its formation is favored by GG-
rich sequences (at high salt concentrations) and cytosine methylation (at low salt
concentrations). Evidence from yeast suggests that it may play a role in transcription
and recombination.
B-DNA is the most abundant and important one, but recent research indicates that
locally DNA can adopt other conformations. Be aware that other DNA structures
than just the nice and regular B-DNA double helix exists. Recently, proteins have
been identified that recognize particular DNA structures as opposed to a specific
base sequence.
DNA helix is associated with many kinds of proteins: this complex is called
chromatin, the three-dimensional structure of DNA. To fit within a living cell, the
DNA double helix must be extensively compacted into a 3-D conformation, this is
aided by DNA-binding proteins.
RNA structure:
1. The primary structure of a single stranded RNA molecule is much like that of a
DNA molecule.
2. RNA strands range from 20 nucleotides to several thousand nucleotides in
length.
3. In RNA synthesis (transcription), only one of the two DNA strands is used as
template.
4. There are several types of RNA: mRNA, tRNA, rRNA, microRNA, piwiRNA, IncRNA,
siRNA, snoRNA and circRNA.
5. Protein encoding RNAs and so-called ‘non-coding’ RNAs.
Although RNAs often consists of a single strand they can easily adopt a double-
stranded structure, happens very frequently and that’s how RNAs perform their
function. So, single-strandedness is not a typical or unique property of RNA.
, RNAs kink, bend, loop and twist themselves into a wonderful variety of shapes. RNAs
lack the chemical diversity of proteins, but many conformational degrees of freedom
of its phosphate backbone, such as a unique hydrogen-bonding and stacking of
nucleotide bases.
Although usually single-stranded, RNA molecules can form short double-stranded
regions, this secondary structure is due to complementary base pairing.
RNA double helices typically are right-handed and have the A form with 11 to 12
base pairs per turn.
Different types of RNA secondary structures are possible. Intramolecular base
pairing: 2 different RNAs can locally base pair by which the 2 RNA are brought
together.
Several factors contribute to the tertiary structure of RNA, for example base-pairing
and base stacking within the RNA itself and interactions with ions, small molecules
and large proteins.
Lecture 2: Chapter 12 Gene transcription and RNA modification
Prokaryotic cells have a nucleoid where they store their DNA, eukaryotic cells do not
have a nucleoid, there DNA roams around free in the cytoplasm.
DNA replication makes DNA copies that are transmitted from cell to cell from parent
to offspring.
Transcription produces an RNA copy of a gene. Messenger RNA is a temporary copy
of a gene that contains information to make a polypeptide.
Translation produces a polypeptide using the information in mRNA. Polypeptide
becomes part of a functional protein that contributes to an organisms’ traits.
The central dogma of molecular biology states that such information
(DNA/RNA/Protein) cannot be transferred from protein to either protein or nucleic
acid.
A general transfer of information is one which can occur in all cells. DNA->DNA, DNA-
>RNA, RNA->protein.
A special transfer of information is one which does not occur in most cells, but may
occur in special circumstances (e.g., viruses). RNA->DNA, RNA->RNA.
A gene is the segment of DNA that contains the information to make a functional
product, which can be either a protein or an RNA. The DNA base sequences define
the beginning and end of a gene and determine to a great extent the regulation of
RNA synthesis (when, and how much, or in which cell type a gene is transcribed).
Gene expression is the overall process by which the information within a gene
results in the production of a functional product (RNA/protein), causing a particular
trait, in conjunction with the environment. Gene expression = RNA transcription +
RNA processing (e.g., splicing, degradation) + RNA translation (=protein synthesis) +
protein degradation.
An important structure for transcription are regulatory sequences, which are sites
for the binding of regulatory proteins; the role of regulatory proteins is to influence
the rate of transcription. Regulatory sequences can be found in a variety of locations.
These regulatory are called promoters in eukaryotes.
The terminator signals the end of transcription.
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