Intro Bio CORRECTIONS CORRECTIONS CORECTIONS
Last Updated on 11/15/09 Most recent corrections are at the top Corrections to problem book are in order of questions.
Corrections to Recitation Problems
11/15/09 RP #8, Question 3D-4. The version posted on the F2401 web site is correct. The version handed out in C2005 recitation had 'codon' instead of 'anticodon.' The question should read: What is the most likely anticodon in the tRNA for GAU?
Clarifications to lecture notes of Fall 2009.
11/5/09 Lecture 15 of 11/5. Two corrections:
1. Numbering. Sections were not labeled properly -- there were two sections labeled 'II'. Sections have been renumbered.
2. Section III C-4 (II C in older version) -- How the repressor protein gets on (or off) the operator. The details of the process described in section III C are beyond the scope of this course. However the information is included because students always ask about it. This section was updated shortly before the lecture, because more experimental evidence has come in. (The older notes had explanation a below; the new ones have both a and b.) The changed section is highlighted in blue both below and in the lecture notes. A minor change was also made in III D; that change is highlighted in blue in the notes, and will be repeated (correctly) in lecture 16. Note that the change is about material that is FYI only. If you printed the notes before the morning of the lecture, you have the old version. Here is the corrected version of III C-4:
4. How does repressor get on or off the DNA? The picture on the handout shows that the repressor is either "on" the operator (in rectangle form) or "off" the operator, (in circle form).
There
are 2 basic models for how the repressor gets on or off the operator. They are
described below, but none of the problems in this course require you to know the
difference between the two.
FYI, for those who like the details,
there are two models
for how an effector works:
a. There is an equilibrium between free and bound "sticky" (rectangle form) repressor -- "rectangular" molecules are spontaneously coming on and off. The effector binds to the free repressor (not the repressor bound to the DNA). Binding of repressor and effector shifts the equilibrium between free rectangles and circles, which in turn shifts the equilibrium between free and bound rectangles.
b. The effector binds to the repressor on the DNA, changes its conformation, and causes it to move onto or off the operator. (In this model the repressor is always bound to DNA, but it moves from a random spot where it has no effect to the operator or vice versa.)
Older versions of the notes explained model a, but current evidence favors model b.
Clarifications to lecture notes of Fall 2008.
11/9/08 Lecture 16 of 11/6/08. Section IV, C, 2 -- Host Specificity (of Viruses). A protein on the surface of the virus particle (virion) must be complementary to (and bind to) a protein on the surface of the target (host) cell. Therefore it is the viral protein on the outside of the virion, not the viral nucleic acid on the inside, that generally determines host specificity. Virions come in many shapes. In viruses that have both a 'head' and a 'tail,' like the model virus shown in class, it is usually the tail, not the head, of the virion that binds to the cell surface.
Problem Book, 19th ed., (2009) Corrections Listed in Order of Problems
The following two corrections were overlooked when making the 19th edition. They apply to the two previous editions (18 and 18revised) as well.
8/19/09 Key to Problem 2-20. Note to C: Alpha-helices that form leucine zippers usually have a leucine at every 7th position, not every 3rd or 4th. It was originally thought that the two helices were interdigitated (as in Becker fig. 23-25 (c)) but we now know the two helices line up side by side as shown here or in Sadava fig. 14.15. To see the difference between the two models more clearly, click here.
8/19/09 Problem 7-7, part C. There are several words missing at the beginning of the last sentence. The last sentence should read: "How would you actually do this experiment, i.e., how would you measure...." (This mistake is also in the previous two editions.)
Corrections & Updates for Previous Editions of the Problem Book
If you have the 18th edition, revised, (2008), Click here for updates to the 19th edition.
If you have the 18th edition (2007), Click here for updates to the 18th edition, revised.
If you have the 17th edition, revised (2005) Click here for updates to 18th edition.
If you have the an older edition, click here for updates.
Texts:
Purves (6th ed.):
2) The definition of an exon given in the glossary of the Purves text is incorrect. Similarly, the depiction of exons in Fig. 14.6 could be misleading in that it fails to show the presence of untranslated regions in the first and last exons (before the translation start codon and following the translation termination codon).1) There are errors in the structures of mannose in the Purves text Fig. 3.12, p.44. For mannose, there should be an H pointing down from position 2, not an OH.
Purves text (5th ed.) :
2) The definition of an exon given in the glossary of the Purves text is incorrect. The definition given in the text of Purves (p. 314, col. 2, para.1) is correct.
1) There are errors in the structures of mannose and fructose in the Purves text Fig. 3.11, p.48. For mannose, there should be an H
pointing down from position 2, not an OH. In fructose, there should be an OH above the ring on carbon 2 and an OH above the ring on carbon 3.Becker text (4th ed.)
None found
Becker (old 3rd edition only):
Fig. 15-11 in Becker implies that simultaneous removal of primer and its replacement occurs without adding on to the 3' end of the next fragment. This is an error. In panels 6 & 7 of fig. 15-11, DNA pol I should be extending fragment #2 on the lagging strand to replace the primer on fragment #1. There should be no gap between fragments 1 & 2. Figure 15-9 has a primer being removed incorrectly too.
