Re: PPS questions

Imre Vastrik (i.vastrik@umds.ac.uk)
Mon, 9 Mar 1998 14:18:02 +0000

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

Nonpolar, unable to make hydrogen bonds with (surrounding) water

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

Proline is rigid, because the main chain nitrogen is linked to the "sidechain"

>3. What are the principles underlying amino acid residue side chain
> conformations in proteins?

Amino acid residue side chain conformation is determined by :
-restrictions set by the steric hindrances between side cain and main chain
-interactions with the other side chains of the same molecule

>4. What information, other than the amino acid sequence itself, is
> available in a SwissProt entry?

Source of the sequence
medline identification number and reference
comments i.e. description of possible function
references to nucleotide database entries
keywords
list of structural features
...

>5. Which databases on the Internet would you use to find protein sequence
> patterns associated with specific functions?

PROSITE
BLOCKS
PRINTS

>6. Describe a program or technique which can be used to represent a
> protein structure within a page of HTML.

-hyperlink to .pdb file. Requires that the user has RasMol
-GIF or JPEG image in the web page
-Java(script) applet

>7. Discuss briefly the four building blocks that form DNA and the way
> these are assembled to form a double helix.

DNA is made up of 2'-deoxyadenosine, 2'-deoxythymine, 2'-deoxyguanosine and
2'-deoxycytosine. These consist of the actual base, sugar (2'-deoxyribose)
and phosphate group. Nucleotides in the same strand are linked by phosphate
esters linking the 5' and 3' postions of the neighbouring sugar residues.
The two strands forming the double helix are antiparallel and are held
together with the hydrogen bonds formed between A-T and G-C pairs.

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

rRNA- major structural and functional component of the ribosomes, essential
for protein synthesis
tRNA- adaptors that translate mRNA sequences into polypeptide sequence
mRNA- carries information from DNA to the protein synthesis machinery

>9. What is the structure of the lac operon and indicate how it is
> regulated.

Structure: promoter (CAP site & operator)-lac z-lac y-lac -a-terminator
In the absence of inducer (1,6 allolactose), lac repressor is bound to the
operator in the promoter and thus prevents transcription. Inducer causes
confornamational change in the repressor molecule and releases it from the
operator.
In the absence of glucose, cAMP levels rise. cAMP binds to the catabolite
gene activator protein (CAP), which is only able to bind its site on DNA
(and thus activate transcription) in the presence of cAMP.

>10. What are Signal Recognition Particles?

Recognises the signal sequence in the transmembrane and secreted proteins
as tey are synthetised.

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

The bases are read as triplets (64 different cobinations). AUG is read as
methionine and initiator (if the surrounding is correct). UGA, UAA and UAG
are read as terminators. All the rest is divided by 19 remaining amino
acids.

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

Gly is small and flexible and often critical for retaining correct
structure of the molecule.

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

right-handed alpha-helices: phi: -45...-180
psi: -30...-60
left-handed helices: phi: 20...90
psi: 45...60
beta-strands: phi: -45...-180
psi: 15...-170

>14. Why are anions often bound to the C-terminal of alpha-helices?

Are they? I could think of a reason, whu cations are bound but not anions...

>15. Give three reasons why the substitution of an Asp(D) by a Trp(W) in a
> protein sequence is unlikely.

(i) The codons coding for Asp (GAT, GAC) are very different from Trp (TGG),
i.e. single mutation is not enough to cause this substitution.
if this substitution still somehow happens it is likely to impair structure
and function of the protein because Trp is (ii)bulky and (iii)hydrophobic.

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

Hydrophobic interactions. They are the strongest in these conditions. For
H-bonding and ionic interactions protein molecules have to compete with
hugh excess of water molecules also "willing" to bind same sites.

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

It has got something to do with the carboxyl group of the 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.

Interior: Val, Phe
Exterior: Asp, Lys, His
Anywhere: Gly, Pro

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

No. It would be difficult to reconstruct the the sequence from overlappng
pieces if the sequence is repetitive. Also, separation of cleaved fragments
could be difficult.

>20. Two of the twenty 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, Ile