Term
| Outline the overall structure of biological membrane |
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Definition
The transmembrane segment is characterized by a hydrophobic core sandwiched between two aromatic belt regions that represent the membrane-water-interphase. These are further sandwiched by the hydrophilic membrane surface that is oriented to the aqueous phase of the cell or the environment. |
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Term
| What is the pH of mostly all amino acids under normal conditions? |
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Definition
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Term
| Outline the common features of alpha helix membrane proteins |
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Definition
hydrophobic
right-handed
transmembrane helix 3.6 residues per turn, i+4 → i
the helical structure can satisfy all backbone hydrogen-bonds internally => chemical property is determined by the side chains
no polar groups are exposed on the helical surface if the side chains are hydrophobic |
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Term
| What can break an alpha helix and why? |
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Definition
| Prolin, because it does not contain a classical side chain |
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Term
| What is the size of hydrophobic core of membrane? How many amino acids do we need to create hydrophobic helix with suxh length? |
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Definition
The size of hydrophobic core of the membrane is 3.5 – 5 nm, so to create hydrophobic helix with such length we need at least 6 aas, but in average 15-20 aas. |
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Term
| Which amino acids are predominantly found in the hydrophobic region? |
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Definition
| Amino acids with aliphatic side chain: valin (Val, V), alanin (Ala, A), Leucine (Leu, L), Isoleucin (Ile, I) and phenilalanin (Phe, F) |
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Term
| Which amino acids are found in aromatic belt? |
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Definition
| Tyrosin (Tyr, Y) and Tryptophan (Trp, W) |
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Term
| Why phenilalanin is not found in the aromatic belt? |
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Definition
Phenilalanyn is not in aromatic belt because it lacks OH group, that we can find in tyrosin → phenylalanin are mainly in the core. |
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Term
| Which amino acids can snorkle? |
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Definition
Positively charged amino acids with long hydrophobic chains can ‚snorkel‘ (lysin (Lys, K) , argenin (Arg, R)). |
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Term
| Which amino acids could not snorkle and why? |
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Definition
| Asparagin(Asn, N) and glutamin(Gln,Q) are also charged, but they can not snorkel, because they are too short, and their head will be located in the aromatic belt. Aspartate(Asp, D) and glutamate(Glu,E) not only too short, but also negatively charged. |
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Term
| What is the tilting angle of the alpha helix embedded into the membrane? |
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Definition
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Term
| Describe 3-10 and pi helices |
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Definition
3-10 – Helix (3 residues per turn; I -> i+3 helix , e.g. the fourth TM segment of several six-transmembrane helix channels )
pi – helix (4.1 residues per turn; i + 5 → I, often as bulges within alpha-helices; e.g. Na+/Cl− dependent neurotransmitter transporter) |
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Term
| What are membrane diggining loops? |
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Definition
mono-layer-spanning TM-helices |
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Term
| What are the topologies of membrane-digging loops? |
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Definition
Some proteins contain mono-layer-spanning TM-helices they can occur in different topologies : helix in – loop out, loop in – helix out, helix in – helix break – helix out. |
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Term
| What stabilizaze helix-helix interactions? |
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Definition
Non covalent bonds
Salt regions |
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Term
| Which motifs are often found in alpha helices? |
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Definition
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Term
| What is the gemetrical pattern of distribution of polar and non polar recidues in betta sheets? |
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Definition
Betta-Sheets result in the side chain to point alternately
into perpendicular directions with regard to the backbone
Most porine structures thus consist of alternating polaren and non-polar amino acids. Polar side chains point towards the hydrophilic inside of the channel. Non-polar side chains are in contact with the hydrophobic membrane core |
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Term
| Outline the main features of betta sheets within trans-membrane proteins |
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Definition
| Number of structures and amount of them participating in the formation of betta barrel is highly conserved!Sheets are antiparallel, their number is even, min number = 8. N and C terminus are always inside, inside loops are always smaller than outside loops. |
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