Módulo 1 Flashcards
António
O que são genes parálogos?
Genes present in a particular organism that are related to each other through a gene duplication event (come from the same gene but have different functions)
What is MSA?
Multiple Sequence Alignment. Método computacional que dá highlight a sequência mais longa possível que seja semelhante entre múltiplas proteínas.
O alinhamento múltiplo é a principal ferramenta de pesquisa de semelhanças entre elementos da mesma família.
O que são padrões conservados (Conserved patterns)?
Sequências que surgem do alinhamento e podem ser utilizadas para definir assinaturas que caracterizam uma família ou domínio.
What does the following string represent?
ATOM 400 N ALA A 53 36.594 24.706 31.023 1.00 15.56 N
Protein Data Bank PDB format (text)
400 Atom number
N The actual atom
ALA A Amino Acid chain
53 Amino acid number
36.594 X coordinate
24.706 Y coordinate
31.023 Z coordinate
1.00 15.56 N Factor Beta (Error in the position of the atoms)
O que é Alternative Splicing?
O splicing alternativo é um processo celular no qual os exões do mesmo gene são unidos em diferentes combinações, levando a transcrições de mRNA diferentes, mas relacionados. Estes mRNA podem ser traduzidos para produzir diferentes proteínas com estruturas e funções distintas – tudo a partir de um único gene
What can Alternative Splicing be used for?
It’s a way to use the same gene to encode proteins that are more or less related.
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Why are there more proteins in the cell than there are genes for said proteins? (Example, why does a cell have 100 proteins but only 10 genes?)
Through Alternative Splicing, a gene can encode for different proteins by removing different parts of itself, producing different proteins.
What is a domain?
They are areas of the protein that are more or less different or independent from each other. Sufficiently stable to fold independently.
What is the difference between a domain and a subunit?
A domain is a discrete function and/or structural section of a polypeptide. This differs from a subunit, which is a single polypeptide in a protein which is in turn composed of multiple polypeptides. It is important to note that subunits can have domains
How is it possible for a protein to have 2 subunits but one domain?
For example, if both subunits have the same function, it can be considered that the protein has only one domain.
Why does automatic genome annotation work?
Because similar sequences imply similar functions.
What is the basis for our understanding how structural domains evolve in proteins?
Similar sequences imply similar structures.
What happens when we have a lower sequence similarity?
Higher structure dissimilarity
Why is the function of an enzyme easy to estabilish?
Because they catalize the same reaction
What does %ID measure? What about RMSD?
%ID: Sequence Similarity
RMSD: Structure Similarity
What happens to the RMSD when proteins are similar?
Tends to be lower
What are some measurements of RMSD?
Posições mais semelhantes de aa
Distância entre alfa-C nas cadeias peptídicas, média do quadrado da distância
What is the seed alignment?
The alignment we use first. A hand-curated alignment of known members of the family
What is the structural unit of the protein?
The domain.
The number of possible domain folds known so far is theoretically finite but in reality it’s practically infinite. True or false?
False. Very large but seems to be finite
O que são domain folds?
O número de formas diferentes de empacotar os elementos da estrutura secundária nos domínios.
Sequence based predictions predict structural features based on the secondary structure, the aminoacid sequence. True or false?
False. It’s the primary structure, (aa sequence)
Give an example of a false positive in a deterministic pattern
The sequence verifies the pattern although it has the rarest possibilities in all of the amino acids
