Lecture 2

Question 1

What is divergent evolution?

Answer 1

Starts from common ancestor and diverge

Question 2

What is convergent evolution

Answer 2

No common ancestor become more similar

Question 3

What causes functional similarity?

Answer 3

not sequence similarity or functional similarity it is the fact that they are ralated through divergent evolution

Question 4

How can you detect homology?

Answer 4

sequence based, structure based or position based

Question 5

When are two sequences homologous

Answer 5

Alignment used: alignment similarity of above 25%

Question 6

Which alignment values are useful?

Answer 6

Raw result: Not useful for similarity just gives best alignment
E-value: useful for judging significance of homology
p-value: nearly identical to E-value

Question 7

What is evolutionary correspondence?

Answer 7

Corresponding residues are derived from a common precursor of the ancestral gene

Question 8

What is structural correspondence?

Answer 8

corresponding residues occupy analogous positions in the 3D structure

Question 9

What is functional correspondence?

Answer 9

corresponding residues fullfill the same role in both proteins

Question 10

Why are proteins better conserved than DNA?

Answer 10

Genetic code degeneracy
AA similarity / exchange frequency

Question 11

How to predict a teritary structure?

Answer 11

Homolgy modelling (look at known structures and sequences and compare to new sequence), Fold recognition (comparison to many candidate templates and judged by structural aspects)

Question 12

What is to be considered in machine learning datasets?

Answer 12

Training, Validation, Testing dataset. Training must be sufficiently diverese to avoid overfitting and out of scope cases.

Question 13

How can you determine the structure of a protein experimentally?

Answer 13

X-Ray cristallography, Alphafold, NRM (Nuclear Magnetic resonance), Cryo EM

Question 14

What is a downside of X-ray cristallography?

Answer 14

Frozen snapshot -> no flexible regions visible

Question 15

What are coiled coil regions

Answer 15

long amphipathic helics with heptad repeat pattern

Question 16

What is 3.6 aa

Answer 16

One helix turn (One heptad repeat is 7 aa) slightly less than 2 turns

Question 17

What are domains and why are they important?

Answer 17

often carriers of unit functionality (functional domains)
protein function can be deduced from domain function
Often subject to independent evolution

Question 18

What is neo-functionalization?

Answer 18

often consequence of gene duplication can be mild or drastic

Question 19

How to define a new motif?

Answer 19

Data: experimental indentification of relevant proteins (ER-targeting) + AA frequencies
Step 1: AA groups with high information content
Step 2: Calculate enrichment factor + significance

Question 20

How to calculate the enrichment factor

Answer 20

In a group of 100 lumenal ER proteins, 20 contain the motif K-D-E-L>
The proteome comprises 25000 proteins, of which 200 contain K-D-E-L>
Enrichment factor = (20 * 24720) / (80 * 180)

Question 21

What is hydrophobicity in aqueous solution

Answer 21

hydrophobic core more hydrophobic than exposed residues

Question 22

What is hydrophobicity in lipid solution

Answer 22

hydrophobic core less hydrophobic than exposed residues

Question 23

How do you predict a transmembrane protein?

Answer 23

Classification of AA by hydrophobicity scale
Evaluation of all possible windows by averaged hydrophobicity

Question 24

How do you predict an amphipathic helix

Answer 24

periodicity of 3.6aa -> angle of 100° between consecutive residues (helical wheel diagram)

Question 25

What are the protein folding principles?

Answer 25

Non-polar inside and polar outside (can form hydrogen bonds)

Question 26

What is the primary structure and how is it connected?

Answer 26

AA chain connected via peptide bonds

Question 27

What is the secondary structure?

Answer 27

Free rotation and rotational angle defines the side chain. Stabilization of secondary structure mostly independent of side chains

Question 28

What is a torsion angle?

Answer 28

The angle of the rotation due to the side chains

Question 29

Why is Glycin special when it comes to torsion angles?

Answer 29

Has no side chain -> therefore less restricted

Question 30

What stabilizes the tertiary structure?

Answer 30

electrostatic attraction, Hydrogen bridges and Van der Waals forces

Question 31

What could exposed hydrophobic residues indicate in a protein?

Answer 31

Interaction surfaces

Question 32

Why are protein sequences better suited for analysis?

Answer 32

Shows you: protein structure, function and localization -> establishes evolutionary relationship

Question 33

What is the ER retention signal

Answer 33

KDEL

Question 34

What can be complications with signal detection?

Answer 34

signal can be remote (outside of detection)
Mechanism can have mutliple signals
Multiple components not orthogonal

Question 35

What is proteomics used for?

Answer 35

Detection proteomics: Which proteins are there, which part of the protein -> changes in protein abundance
Modification proteomics: PTMs, are there changes in modification levels
Interaction proteomics: Which proteins bind to each other…

Question 36

Methods for protein detection

Answer 36

Gel Electrophoresis, MS, Antibodies (Wester blot)

Question 37

What is two dimensional Gel electrophoresis

Answer 37

1. Isoelectric focussing (seperates by charge)
2. SDS-page (seperates by size)