BIO111 - Molecular genetics - Keywords

Pyrimidine, pairs with Guanine

Has the follwing structure: 

Pyrimidine, pairs with Adenine. Exists only in the DNA. 

Has the follwing structure: 

Nucleoside consisting of the base Adenine and a sugar: 

- 2' deoxyribose = deoxyadenosine

Nucleoside consisting of the base Guanine and a sugar

Nucleoside consisting of the base Cytosine and a sugar

Nucleoside consisting of the base Thymine and a sugar

Each phosphate in a DNA chain makes two ester bonds: 

- one with the 3' carbon of one deoxyribose

- one with the 5' carbon of the next sugar

This gives a nucleotide chain a polarity. A phosphate attached to the 5'-most sugar at one end (5') and a free -OH on the most 3' sugar at the other end of the chain (3' end). 

Connection of two bases (Adenine - Thymine (2H Bonds) and Cytosine - Guanine (3H Bonds)) via H-Bonds in the DNA helice. 

As the bases of each DNA chain are complementary to each other (Adenine - Thymine and Cytosine - Guanine), this leads to two different strands. These two strands are, as the base pairs, complementary to each other. 

The two DNA strands twist to form a right handed double helix. As the two "backbones" are not exactly opposite to each other, different amounts of space are created:

- On one side there is more space = major groove 

- On the other side there is less space = minor groove

Complex of DNA and proteins (half of which are histones). DNA and histones make up the nucleosomes, which are being chained together. 

With this structure, the DNA chains are condensed to a 10'000 to 50'000 fold of their lenght, which allows them to fit into the nucleus. 

During mitosis and meiosis, the chromatin condeses to chromosomes. 

After DNA strands are supercoiled, they are wrapped around histone nucleosomes. These contain 8 histone protein molecules: 

- 2 H2A

- 2 H2B

- 2 H3

- 2 H4

In eukaryotes, DNA is wrapped around histone nucleosomes. The DNA makes two turns around each nucleosome = 146 bp. These nucleosomes contain 8 histone protein molecules: 

- 2 H2A

- 2 H2B

- 2 H3

- 2 H4

In supercoiling, topoisomerases coil the dsDNA around its own axis (same direction as helix = positive or opposite direction of the helix = negative) in order to make it take up less space. 

It can be reduced by: 

- Gyrases or topoisomerases

- Physical nicking of the strand

The process of replicating the DNA in order to double the informational content before meiosis or mitosis.

The DNA replication is semiconservative (results in each daughter molecule inheriting one old and one new strand). 

The template is a source strand (ssDNA) of which a complementary DNA or RNA strand is synthesized. 

Origin of replicatioin, also called ORI or Origin, is the place on the DNA molecule where the replication starts

Enzymes which elongate DNA chains. For this process they need: 

- Template (ssDNA)

- Activated (triphosphate) forms of the four dNTPs

- An existing chain to elongate

In e. coli the main polymerase is pol III. In mammals it is the DNA pol delta. 

These enzymes are highly processive. 

Deoxynucleotidetriphosphate

Some polymerases have a proofreading activity. They can read the DNA strand from 3' to 5' (exonuclease) in order to "proofread" them. This is necessary after a misincorporation in the 5' to 3' direction. 

Enzyme that unwinds the dsDNA in order to let it be replicated by the polymerase. It does this by breaking open the H-Bonds between the basepairs.

As the polymerase is not able to create a strand but only to elongate it if it's already existing, the primase creates a short RNA strand (ca. 10 nt. long) directly on a ssDNA template. These short strands of RNA are called "primers" and can then be extended by DNA polymerases. 

Short RNA strand (ca. 10 nt.) which is replicated directly from a ssDNA strand by primase. This is done in order to give the polymerases something to replicate. 

As during DNA replication, both strands are used as templates, the dsDNA has to unwind. This is done by breaking the H-Bonds between the base pairs (helicase). The DNA pol advance and the DNA is contiuously unwound to generate these two template strands. This creates a replication fork. 

Due to the polarity of the DNA synthesis, synthesis of one strand proceeds from left to right, and on the other strand from right to left. 

The strand on which the synthesis is in the direction of the replication fork is called the leading strand, the other the lagging strand. 

Strand which is sythesized in direction of the replication fork. The synthesis on this strand is not interrupted

Strand which is synthesized away from the replication fork. This leads to a discontinous synthesis. In order to rectify this, DNA primase must regularly make new primes, as DNA pol synthesizes the new strand. The interrupted fragments of newly synthesized DNA are called Okazaki fragments. 

The new strands consists of Okazaki fragments (joined together by DNA ligase) and RNA primers (will be removed by a yet unclear mechanism)

Region of repetitive nucleotide sequence at each end of each chromosome. Contains "telomeric repeats" (G-rich) which protect the "important DNA" during cell division. This is necessary because of the "end replication problem". 

While the 3' end of a newly synthesized strand can be completely replicated, the requirement for an RNA primer prevents complete replication of the very 5' end of the lagging strand. 

Enzyme containing a small RNA template. This template can base pair with the free 3' end of the parental strand opposite the 5' end of the newly synthesized lagging strand. This allows to elongate the telomeric repeats. 

In humans, telomerase is present only in germ and stem cells. 

The central dogma states, that in all living organisms, genetic information flows from DNA to RNA to proteins in a unidirectional pathway. It allows three types of information flows: 

- DNA replication (DNA to DNA)

- Transcription (DNA to RNA)

- Translation (RNA to Proteins)

There are few exceptions to the central dogma (e. g.): 

- Rna can make RNA (RNA viruses)

- RNA can make DNA (telomerase)

Transcription is the synthesis of RNA from a DNA template. 

Requirements are: 

- ssDNA template

- Activated (triphosphate) nucleotide precursors

- Transcription proteins (RNA polymerases)

Directs the information encoded by a gene (made of DNA) to the synthesis of a protein (main task). 

Contains (usually) only one strand and is thus very flexible. 

Composed of 4 nucleotides: 

- AMP, GMP, CMP and UMP (Uracil + Sugar + Phosphate)

Has a 5' to 3' polarity. 

Nucleotide. Able to pair with Adenine and Guanine (rare). 

Has the following structure: 

RNA molecules that have a catalytic aktivity.