Thank-you for the answers,
Yours sincerely,
Jim Pitts.
Tobias Bundy wrote:
> 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.