Plasmid

A circular double-stranded DNA molecule, which is non-essential to the life of the cell. It is typically found in bacteria, yeast and a few superior eukaryotes, thus establishing a symbiotic or parasitic relationship with its host cell.

Plasmids can appear in different configurations that vary from fully intact to linear, when they have free ends. They can also exist in super-coiled structure, the most compact form of this molecule. They vary in size from 1 to 250 Kb.

There are two known replication strategies related to plasmids: non-integrative and integrative (fig.1). Non-integrative replication occurs, when a plasmid replicates independently, due to the possession of at least one DNA sequence, which is able to initiate replication. Other plasmids, called episomes, have the ability to insert themselves into bacterial chromosomes and they can maintain this form through several cell divisions. This is known as integrative replication.

 

Fig. 1 - Replication Strategies for (a) a non-integrative plasmid and (b) an episome

 Plasmids can be transferred between bacteria through host-to-host transfer, which is called horizontal gene transfer. This is an important process for the host cell, because it can provide selective advantages such as resistance to antibiotics.

They are important molecules in molecular genetics and are often used as a tool to clone, transfer and manipulate genes. Plasmids that are used experimentally for these purposes are called vectors.

 References:

Nature.com, (2015). plasmid / plasmids | Learn Science at Scitable. [online] Available at: http://www.nature.com/scitable/definition/plasmid-plasmids-28 [Accessed 29 Oct. 2015]

Brown, T. (2010). Gene cloning and DNA analysis: an introduction. (Chapter 2). John Wiley & Sons.

Watson, J., Gilman, M., Witkowski, J. (1992). Recombinant DNA. Nova Iorque: Scientific American Books

Thomas, C. M. and Summers, D. 2008. Bacterial Plasmids. eLS. 

Licenciatura em Bioquìmica / 2º Ano

Turno 3 Grupo 4

Ana Micaela Lavender

Bruna Araujo

Helena Vaz

Mário Azevedo

Nuno Santos

Reverse transcriptase

Reverse transcriptase (fig. 1) is a protein, belonging to the class of enzymes class, whose function is to generate complementary DNA (cDNA) from an RNA template. The mechanism is named reverse transcription. In other words, this enzyme polymerises DNA molecules from RNA, giving origin to a complementary nucleotide sequence.

Figure 1 : Tridimensional format of the enzyme reverse transcriptase.

 (Source: https://pt.wikipedia.org/wiki/Transcriptase_reversa#/media/File:Reverse_transcriptase_3KLF_labels.png)

Inês Dias, a73579

Sofia Pinto, a74770

Tiago Silva, a73919

                                                      G 3.4

                

Satellite DNA

Satellite DNA or tandemly repeated DNA are DNA sequences highly repetead present on heterochromatin and also found at centromeres, being made up by short and simple sequences that form big sequence blocks. It is a common feature of eukaryotic genomes but is found less frequently in prokaryotes. 

They are known as satellites because DNA fragments containing tandemly repeated sequences form different bands when genomic DNA is fractionated by density gradient centrifugation.

There are two types of satellite DNA, known as microsatellies and minisatellites, where microsatellites clusters are shorter than minisatellites. For example, Huntington’s disease it’s due to the (CAG)n sequence extension caused by microsatellite CAG in the gene enconding for the huntingtin protein.

Alu elements

A small portion of DNA repeated several times, mostly in primate genomes, accounting for 11% of the human genome. It is a retrotransproson, the most abundant moving element in human genome and it derivates from 7SL RNA (portion of rRNA). Its first appearance coincides with the origin of primates and it plays a major role on gene expression as they contribute to genome evolution, gene regulation and is related to several diseases.

Nowadays, Alu elements are about 300 base pairs long, so they are considered short interspersed elements (SINEs).

They are a common source of mutations mostly in the non-coding DNA regions (the mutation usually does not cause any difference in the phenotype). However, the variation generated can be used in studies of the movement and ancestry of human populations.

References:

(2015). Retrieved 26 October 2015, from http://www.genomebiology.com/content/pdf/gb-2011-12-12-236.pdf

Wikipedia,. (2015). Alu element. Retrieved 26 October 2015, from https://en.wikipedia.org/wiki/Alu_element

Licenciatura em Biologia Aplicada - 2º ano

Carla Matos

Catarina Ribeiro  

Luís Carvalho

Sofia Faria

Nuclease protection assays (NPAs)

  The nuclease protection assay is a method used in biochemistry and genetics for the detection, quantitation and mapping of specific RNAs in a complex mixture of total cellular RNA. This technique includes both ribonuclease protection assays (RPAs) and S1 nuclease assays.

    The principles of this technique are the hybridization of single-stranded RNA. This is achieved by addition of antisense RNA probe, containing the complementary strands of RNA, to the initial solution containing the RNA. After hybridization, the remaining RNA, which did not hybridize, is removed by adding nuclease. Then, the existing nucleases in the solution are inactivated and, at the same time, the hybridized RNA precipitates. These are separated on denaturing polyacrylamide gel and visualized by autoradiography.

Licenciatura em Bioquímica, 2ºano
Pl 1 – Grupo 3
Ana Catarina Azevedo
Bruna Martins
Eliana Santos
Marta Monteiro
Ricardo Rosa

Ty Elements

Ty elements comprise a family of dispersed repetitive DNA sequences that are found at different sites in different strains of yeast. Ty is an abbreviation for "transposon yeast", it has several features that are unique, and it appears to resemble a primitive retrovirus and it can be found in Saccharomyces cerevisiae . A transposition event creates a characteristic footprint: 5 bp of target DNA are repeated on either side of the inserted Ty element.                                         

 Recombination between Ty elements seems to occur in bursts; when one event is detected, there is an increased probability of finding others. Gene conversion occurs between Ty elements at different locations, with the result that one element is "replaced" by the sequence of the other.

Ty elements terminate in short direct repeats and are transcribed into two overlapping RNAs. They have two reading frames, with sequences related to the retroviral gag and pol genes. 

Only some of the Ty elements in any yeast genome are active: most have lost the ability to transpose (and are analogous to inert endogenous proviruses) and transposon yeast  elements can generate virus-like particles.

Group G1.1 Ana Abreu, Ana Martins, Daniela Garcia, Marta Rocha and Rita Natividade

Ref: Ndsu.edu,. (2015). Transposable Genetic Elements. Retrieved 27 October 2015, from https://www.ndsu.edu/pubweb/~mcclean/plsc431/transelem/trans2.htm

Boeke, J. D. et al. (1985). Ty elements transpose through an RNA intermediate. From http://webcache.googleusercontent.com/search?q=cache%3Ahttp%3A%2F%2Fgenes.atspace.org%2F16.4.html&gws_rd=cr&ei=4SkuVqyYCoWbU6S6jvgB

Retrovirus pol Gene

pol gene is one of the main segments of retroviral RNA. It encodes four main viral proteins: protease, RNase H, integrase and the most importante one, reverse transcriptase. The latter plays an important role by copying the virus’ RNA into DNA, which is unique in retroviruses. This enzyme is a remarkable factor in the life cycle of HIV, also a retrovirus.

Reference: Stowell, D. (2006). Molecules of HIV (pol). Retrieved December 27, 2015, from http://www.mcld.co.uk/hiv/?q=pol

Licenciatura em Biologia Aplicada - 2º ano:
Grupo 2 PL3
David Miziuc  
Inês Fernandes 
Inês Lages
Tiago Ferreira

Polycistronic mRNA

Polycistronic mRNA (fig. 1) is a messenger RNA molecule that encodes the sequence for more than one protein usually with a related funcion. This molecule emerges from the transcription of operons which are a set of several genes activated by the same promotor. It acts on the translation process (protein synthesis) in procaryotes. In some cases, this messenger RNA can be cleaved into individual messengers that can be translated individually.

                                   

                                                                                          1. Prokaryotic polycistronic transcription unit

Licenciatura em Bioquímica, 2º ano:

Grupo 1 PL3

Ana Isabel Baptista

Bruna Basto

Eduarda Gomes

Gonçalo Carvalho

Luís Peixoto

Tiago Gião