29 Jul WHICH RESIDUES WOULD YOU EXPECT TO FIND IN A CALCIUM BINDING SITE?
Does
a positive change or a negative change in free energy indicate a favorable
(spontaneous chemical event)?
2)
If
some spontaneous event is endothermic, what must have been the “driving force”
behind that event?
3)
Given
the free energy changes given for coupled reactions that result in the
conversion of glucose to glucose 6-phosphate (slide 19). What are the K’eqvalues
for each separate reaction and the overall reaction? How does the mathematical
relationship between ∆G’° values compare to that between K’eqvalues?
4)
Explain
why energy is released when ATP is hydrolyzed and why energy is absorbed when
ATP is formed from ADP and Pi.
5)
Which
residues would you expect to find in a calcium binding site?
6)
Would
you expect to find the Gln side chain acting as a hydrogen bond donor or
acceptor?
7)
Why
is His often found in the active site of enzyme active sites?
8)
Why
is protein concentration often measured using A280?
9)
Medical
Rejuvenation Clinic Australia Pty Ltd (co-owner/director Stephen Dank) sells
Bremelanotide (PT 141) which was developed from the peptide hormone Melanotan
II, which underwent testing as a sunless tanning agent. In initial testing,
Melanotan II did induce tanning, but caused sexual arousal and spontaneous
erections in male volunteer test subjects. Based on the figure below: (a) What
amino acids side chains do you recognise, give names, single letter and three
letter codes? (b) does it contain any unnatural amino acids? (c) Based on the
ionisation status of the functional groups in this figure, what can you say
about pH?
10)
Draw
a tripeptide with one peptide bond transand one cis. Name the
amino acids and give their three- and single-letter codes.
11)
Draw
Ramachandran plots to indicate which region you would find plotted most of the
residues in (a) human growth hormone (hGH) and (b) the its receptor (hGHR)
12)
Medical
Rejuvenation Clinic Australia Pty Ltd (co-owner/director Stephen Dank) sells
the peptide AOD 9604, sequence YLRIVQCRSVEGSCGF, a peptide from the C-terminus
of Human Growth Hormone (HGH), with an added N-terminal tyrosine. When
administered by subcutaneous injection would you expect it to maintain a
disulfide bond (why/not)? Which residues have the potential to form salt
bridges? What overall charge would it carry (show reasoning)?
13)
Does
disulfide bonding direct folding or does folding direct disulfide bond
formation? Discuss the evidence.
14)
Ideally,
protein folding is encoded in the amino acid sequence alone. Why then do cells
have, and need chaperones?
15)
Based
on what you know about amino acid side chains, devise an experiment to measure
the thermal stability of a protein ~150 amino acids long
16)
Discuss
the role of backbone to backbone hydrogen bonding of the polypeptide in terms
of the energetics of protein folding.
17)
How
do the linear patterns of polar and nonpolar residues in an amino acid sequence
relate to how they project from (i) beta-strands (ii) alpha- helices?
18) The natural
“handedness” of protein secondary structure we observe on Earth (displayed in a
Ramachandran plot) is because the naturally occurring amino acids are L-amino
acids. What would the Ramachandran plot look like for a planet where the
naturally occurring amino acids are D-amino acids?
19)
Antibodies
are Y-shapes heterotetramers composed of two light chains and two heavy chains
. Discuss the secondary, tertiary and quaternary structure of antibodies.
20)
Define
the term “protein domain” in terms of folding and structure.
21)
What
are four genetic mechanisms that can give rise to new proteins with new
functions?
22)
Describe
one or more experiments that could test whether a protein contains one or more
domain.
23)
What
is the difference between sequence identity and sequence similarity? Give an
example of similarity.
24)
What
is the general threshold of sequence identity that allows us to make firm
predictions about the fold of a protein?
25)
If
two proteins share the same overall fold, what can you say about their
ancestry?
26)
Define
the term “protein domain” in terms of folding and structure.
27)
What
are four genetic mechanisms that can give rise to new proteins with new
functions?
28)
Describe
one or more experiments that could test whether a protein contains one or more
domain.
29)
What
is the difference between sequence identity and sequence similarity? Give an
example of similarity.
30)
What
is the general threshold of sequence identity that allows us to make firm
predictions about the fold of a protein?
31)
If
two proteins share the same overall fold, what can you say about their
ancestry?
32)
Explain
the structural features that would
account for the different melting points for this 18C fatty acid series: ‘Stearic acid
69.6oC’;
‘Oleic acid 13.4oC;
‘Linoleic acid -5oC;
‘Linolenic acid -11oC.
33)
How
many triaglycerol species are
theoretically possible using palmitic acid (16:0) and oleic acid (18:1’9)? Rank these
triaglycerols by their expected melting point.
34)
The
box cartoon representation depicts the
overall organization of a triacylglycerol. The lines between the boxes
denote chemical bonds. What are the chemical names for these bonds?
35)
Draw
equivalent representations of 2 other classes of lipids that also contain
glycerol. Annotate the diagram with the chemical names for the different
chemical component of these lipids.
36)
Draw
equivalent representations for 2 main
groupings of sphingolipids, and again
indicate the
different chemical groups within the sphingolipid.
37)
Sodium
dodecyl sulfate (SDS) is an anionic detergent open used in biochemistry. Its
structure is a single 12C chain with a negatively charged sulfate “head group”.
What packing arrangement wills ‘SDS’ adopt in aqueous solution?’
38)
Predict
the outcomes of mixing solutions of – SDS with free fatty acids and SDS with
phospholipids .
39)
Integral
membrane proteins have a transmembrane domain/sequence that in many (but not
all) cases is alpha helical in structure. Knowing that a membrane’s phospholipid
bilayer is approximately 3nm thick, and that each turn of an alpha helix
contains 3.6 amino acids and spans 0.54nm, how many residues are needed in an
alpha helix to cross a membrane?
40)
Is
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