Re: PPS questions

Tobias Bundy (bundy@fak-cbg.tu-muenchen.de)
Mon, 16 Mar 1998 17:13:35 +0100 (MET)

1.) Define the term "hydrophobicitiy" (when used in relation to amino
acids and proteins)

The term refers to neutral, nonpolar and aliphatic or aromtaic structures,
which occur as sidechains of amino acids. Because these hydrophobic
structures are unable to make hydrogen bonds with the surrounding polar
solvant (i.e. water), they are mainly found within the protein.

2.) Why is the amino acid proline often referred to as a "helix breaker" ?

Proline has a cyclic sidechain in which the nitrogen bonded, so it can't
make hydrogen bonds to the previous or following amino acid.

3.) What are the principles underlying amino acid residue side chain
conformation in proteins ?

the side chain conformation isdetermined by the side chain itself
respectivly the steric relation to each other (i.e. Prolin, S-S-bonds).
these steric hinderences may as well occur between the amino acid side
chains and the protein's backbone

4.) What information other than the amino acid sequence itself, is
available in a swissprot entry ?
Available are :
- Comments like the description of possible function of the protein
- Refenerences to entries in nucleotide databases
- Medline identifiacation number
- A list of structural features

5.) Which databases on the internet would you use to find protein sequence
patterns associated with specific functions ?
- PROSITE

6.) Describe a programm or technique which can be used to represent a
protein structure within a page of HTML
The first possibilty is to embed an image in the website, and the second
one to construct a hyperlink to some graphics file like *.pdb. This
however requires that the user has chemical mime as well as the appropiate
viewer (i.e. RASMOL) installed.

7.) Discuss briefly the 4 binding blocks that form DNA and the way
these are assembled to form a double helix
The binding blocks are :
- 2'-Deoxyadenosine
- 2'-Deoxythymine
- 2'-Deoxyguanosine
- 2'-Deoxycytosine
In these blocks the 4 bases (adenine, thymine, guanine, cytosine) are
bound to 2'-Deoxyribose. The nucleotides themselves are connected to
strands which are formed by the Deoxy-sugar and phosphate esters that
connect to the deoxyribose at their 3' and 5' positions. The DNA in this
way forms some sort of ladder, in which the Bases in combination of A-T
and C-G act as stairs.

8.) Indicate the different roles within the cell of tRNA, rRNA and mRNA

- m-RNA
It serves as a copy of a prot of one DNA-strang (gene). Its task is to
transport information from the nucleus to the ribosomes.

- t-RNA
RNA possesses a special strucutre which enables it to transport amino
acids. The t-RNA binds one specific amino acid on one end, and the m-RNA
on the other. This leads to the binding of the transported amino acid on
the synthecised protein.

- r-RNA
This sort of RNA is a strucutural component of a ribosome. It posses a
to the m-RNA complementary structure (anticodon).

9.) What is the structure of the lac operon and indicate how it is
regulated
The structure is : Promotor - lac z-lac y.lac - Terminator
In the absence of the inducer (1,6-allolactose), the repressor is bound to
the operator, which is located in the promotor. This prevents
transcrition. The inducer causes change in the conformation of the
repressor moecule and releaes it from the operator.

10.) What are Signal Recognition Particles ?

SPP consist of 6 polypetide chains and one 300-bases-RNA
It works as an identifier for the endoplasmatic reticulum in the synthesis
of sectretory proteins

11.) How do the four bases in mRNA code for 20 amino acids and control
initiation/termination during translation ?

The 20 amino cids are coded through tripletts of RNA-bases, socalled
codons. Certain combination act as start/stop commands, however ther are
certain coversions i.e the start command and the coding for Met

12.) Why are glycine residues often conserved in homologous protein
sequences ?

Gly is the smallest amino sacid and so it is the most felxible in
structural means.

13.) Give the phi/psi tirsion angle limits for right-handed alpha-helices,
beta-strands and left-handed helices

- right-handed alpha helix : phi = -45 - -180
psi = -30 - -60

- beta-sheet : phi = -120 - -140
psi = +120 - +130

- left-handed alpha helix : phi = +20 - +90
psi = +45 - +60

14.) Why are cations often bound to the C-terminal of alpha-helices ?

15.) Give 3 reasons why the substitution of an Asp by a Trp in a protein
sequence is unlikely
- There is great sterically differende between the 2 amino acids
- Asp is acidic, Trp is basic
- The condons coding for Asp respectivly Trp are very different

16.) Which type of interaaction, H-bonding, hydrophobic interactions or
ionic interactions, is likely to be the most important in energy
terms in causing protein molecules in dilute aqzeous solution to
associate with each other ? Why ?

Hydrophobic interactions play the most important role in protein
association, because there is no "competition" like in H-bonding or
hydrophobis interactions from the sorrounding water.

17.) Why is the pKa of the epsilon-amino group higher than that of the
alpha-amino group of Lys ?

18.) Which of the following amino acids are likely to be found in the
interior of a protein and which on the exterior : Val, Pro, Phe, Asp,
Lys, His, Gly

- Intierior : Val, Pro, Phe
- Exterior : Asp, Lys, His

19.) Histones have high percentages of basic (Arg and Lys) amino acids.
Will it be easy to determine their sequence by peptide mapping ?
Why or why not ?

The sequence of the histones is repititve, so that it would be difficult
to rearrange the fragments in the right order.

20.) 2 of the 20 amino acid residues which occur in proteins have side
groups which contain asymmetric carbons. Which are they and what is
the R/S classification of each asymmetric centre ?

- Thr : R-classification
- Ile : S-classification

In both amino acids the asymmtric carbnons are the Beta-Carbons.