Módulo 1

Question 1

O que são genes parálogos?

Answer 1

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)

Question 2

What is MSA?

Answer 2

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.

Question 3

O que são padrões conservados (Conserved patterns)?

Answer 3

Sequências que surgem do alinhamento e podem ser utilizadas para definir assinaturas que caracterizam uma família ou domínio.

Question 4

What does the following string represent?

ATOM 400 N ALA A 53 36.594 24.706 31.023 1.00 15.56 N

Answer 4

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)

Question 5

O que é Alternative Splicing?

Answer 5

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

Question 6

What can Alternative Splicing be used for?

Answer 6

It’s a way to use the same gene to encode proteins that are more or less related.

Question 7

NEXT

Answer 7

NEXT

Question 8

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?)

Answer 8

Through Alternative Splicing, a gene can encode for different proteins by removing different parts of itself, producing different proteins.

Question 9

What is a domain?

Answer 9

They are areas of the protein that are more or less different or independent from each other. Sufficiently stable to fold independently.

Question 10

What is the difference between a domain and a subunit?

Answer 10

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

Question 11

How is it possible for a protein to have 2 subunits but one domain?

Answer 11

For example, if both subunits have the same function, it can be considered that the protein has only one domain.

Question 12

Why does automatic genome annotation work?

Answer 12

Because similar sequences imply similar functions.

Question 13

What is the basis for our understanding how structural domains evolve in proteins?

Answer 13

Similar sequences imply similar structures.

Question 14

What happens when we have a lower sequence similarity?

Answer 14

Higher structure dissimilarity

Question 15

Why is the function of an enzyme easy to estabilish?

Answer 15

Because they catalize the same reaction

Question 16

What does %ID measure? What about RMSD?

Answer 16

%ID: Sequence Similarity
RMSD: Structure Similarity

Question 17

What happens to the RMSD when proteins are similar?

Answer 17

Tends to be lower

Question 18

What are some measurements of RMSD?

Answer 18

Posições mais semelhantes de aa
Distância entre alfa-C nas cadeias peptídicas, média do quadrado da distância

Question 19

What is the seed alignment?

Answer 19

The alignment we use first. A hand-curated alignment of known members of the family

Question 20

What is the structural unit of the protein?

Answer 20

The domain.

Question 21

The number of possible domain folds known so far is theoretically finite but in reality it’s practically infinite. True or false?

Answer 21

False. Very large but seems to be finite

Question 22

O que são domain folds?

Answer 22

O número de formas diferentes de empacotar os elementos da estrutura secundária nos domínios.

Question 23

Sequence based predictions predict structural features based on the secondary structure, the aminoacid sequence. True or false?

Answer 23

False. It’s the primary structure, (aa sequence)

Question 24

Give an example of a false positive in a deterministic pattern

Answer 24

The sequence verifies the pattern although it has the rarest possibilities in all of the amino acids

Question 25

Give an example of a false negative in a deterministic pattern

Answer 25

The sequence verifies everything in the pattern except one completely unexpected amino acid.

Question 26

What are some downsides of DP?

Answer 26

Extremely high rigidity, which means it doesn’t accept any deviations to the pattern.

Question 27

What is a Confusion Matrix?

Answer 27

A Table with two rows and two columns that reports the number of true positives, false negatives, false positives, and true negatives

Question 28

Num classificador binário, a sensibilidade é dada pela taxa de verdadeiros positivos e a especificidade é dada pela taxa de falsos negativos. Verdadeiro ou falso.

Answer 28

FALSO. A especificidade é dada pela taxa de verdadeiros negativos.

Question 29

A consensus sequence is likely a true positive. True or false?

Answer 29

True.

Question 30

Name one big advantage of PSSM.

Answer 30

It has a lot less false negatives because it can put any amino acid in any position

Question 31

What’s PSSM and what’s its deal?

Answer 31

Position specific scoring matrix attributes a value to each amino acid, and depending on the score they receive, they conclude if the sequence belongs or not to a certain family or domain.

Question 32

PSSM attributes a score of 0 to any gap/transition in the sequence. True or false?

Answer 32

False. It does not attribute scores to gaps/transitions.

Question 33

PSSM doesn’t attribute a score to any gaps in the sequence, but it does attribute weight. True or false?

Answer 33

True

Question 34

In a weight matrix, the higher the score between two aminoacids, the higher the chances of them being interchangable. True or false?

Answer 34

True

Question 35

What is homology modelling?

Answer 35

The use of information from homologous proteins from databases and other sequences to model a protein.

Question 36

What are the three mains steps of homology modelling?

Answer 36

Alignment and superposition with the reference structure, improvement and preliminary structure, and optimization of energy.

Question 37

Swiss model is unreliable only in the position of loops and the side groups of amino acids, and is only reliable for the position of the backbone (alfaCarbon)

Answer 37

True

Question 38

What is the Rosetta Method?

Answer 38

Splitting a sequence into several shorter sequences, and trying to fill the gaps with “randomly generated” sequences, until something fits.

Question 39

Alphaphold is so good it’s similar to structures provided by…

Answer 39

X-Ray crystallography

Question 40

Num classificador binário, a sensibilidade é dada pela taxa de verdadeiros positivos e a especificidade é dada pela taxa de verdadeiros negativos. Verdadeiro ou falso

Answer 40

Verdade

Question 41

Num classificador binário, a especificidade é dada pela taxa de verdadeiros positivos e a sensibilidade é dada pela taxa de verdadeiros negativos. Verdadeiro ou falso

Answer 41

Falso.
Sensibilidade é dada pela taxa de verdadeiros positivos
Especificidade é dada pela taxa de verdadeiros negativos

Question 42

O que significa pontuação (local) de QMEAN4

Answer 42

O QMEAN4 é uma função de scoring usada assessar a qualidade da previsão de modelos de estrutura proteica, que compões outras 4 métricas, como a interação entre os Cb, a interação entre todos os átomos, exposição ao solvente e a torsão entre 3 aa consecutivos. Uma pontuação local iria significar a qualidade de previsão de um aa ou local em específico, tendo em conta as métricas.