Intro Bio CORRECTIONS CORRECTIONS CORECTIONS
Last Updated on 08/24/11 Most recent corrections are at the top Corrections to problem book will be in order of questions.
8/24/11 No 2011 corrections yet! Corrections to lectures,
problem book, etc., of 2011 will be posted as soon they are discovered. If you
find any errors, please email one of the instructors. We welcome useful
Corrections & Updates for Previous Editions of the Problem Book
If you have the 19th edition, (revised, 2010), click here for updates to covert to the latest edition -- 19th edition, re-revised (2011).
If you have the 19th edition, (2009), click here for updates to covert to the 19th edition, revised.
If you have the 18th edition, revised, (2008), click here for updates to convert to the 19th edition.
If you have the an older edition, click here for updates.
Corrections to Old Lecture Notes
Clarifications to Lectures of Fall 2010
Modification of original lec. 9 Ppt, html
and pdf files:
Material that was not covered in lecture and for which you are not responsible has been indicated in green italics (html, pdf) or a blue background (ppt).
11/28/10 Lecture 18: III C 2 b -- Oligonucleotide probes. There is a typo in one of the codons. Example should read:
Can't predict exact DNA/mRNA sequence from amino acid sequence. For example, if amino acids are lys - asp - met etc, DNA would be AAG/A GAC/T ATG etc. Don't know if base #3 is G or A; # 6 is C or T etc.
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).
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.
Corrections to Texts (Older Editions):
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.)
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.