Chapter 2
General References
http://www.dnaftb.org/
- "DNA from the beginning" from the Dolan DNA Learning Center at Cold
Spring Harbor Laboratory. Features sections such as "Classical Genetics,"
"Molecules of Genetics," and "Genetic Organization and
Control."
http://www.emunix.emich.edu/~rwinning/genetics/
- Genetics Online from Dr. Bob Winning at Eastern MIchigan University
http://www.mendelweb.org/MWolby.html - An online essay by Robert C. Olby (Department of the History and Philosophy of Science, University of Pittsburgh) on "Mendel, Mendelism, and Genetics."
hal.wzw.tum.de/genglos/asp/genreq.asp?list=1 - A glossary of genetic terms from Dr. Birgid Schlindwein at the Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt at the Technical University of Munich
TABLES
Table 2.1 – see http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html for a similar table and http://www.bio.davidson.edu/Biology/aatable.html for more detailed information.
Table 2.2 – see http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG1 for this table and see http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/temp-strand.html for a good discussion of template versus coding strands of DNA.
Table 2.3 – information from http://www.ncbi.nlm.nih.gov/nuccore/550056.
FIGURES
Figure 2.1 A – Drawing a normal karyogram – Open http://www.cydas.org/OnlineAnalysis/WebExample4.aspx
in a different tab or window so that you will have access to both that site and
the instructions here. In the first box replace:
46,y,-7,+8,t(9;22)(q341;q112),i(17)(q10),+der(22)t(9;22)
with:
46<2n>,XY
The easiest way to make this replacement is to mark
and copy 46<2n>,XY and then past over the selected text
"46,y,-7,+8,t(9;22)(q341;q112),i(17)(q10),+der(22)t(9;22)"
In the "drawing sequence" box replace:
1,2,3,4,5,6,7,X,8,9,10,11,BR,12,13,14,15,16,17,18,19,20,21,22,Y,?
with:
1,2,3,4,5,6,7,8,BR,9,10,11,12,13,14,15,16,BR,17,18,19,20,21,22,X,Y
In the "Banding resolution" radio buttons
select 800 bands. Uncheck the "color" box if you want it in
black and white. Then click the "Draw" button.
Figure 2.1 B – Bands for the fourth chromosome,
see http://www.biologia.uniba.it/rmc/2-YAC-BAC/BAC-Chromosome/ideograms/04.html
Figure
2.2 – Mitosis. This is drawn using a mix of "R" and Powerpoint
©. To use the R scripts you will need to download the package
"ellipse" to, well, draw ellipses.
Rel.Length=
c(8.4, 8, 6.8, 6.3, 6.1, 5.9, 5.4, 4.9, 4.8, 4.6, 4.6, 4.7, 3.7, 3.6, 3.5, 3.4,
3.3, 2.9, 2.7, 2.6, 1.9, 2, 5.1, 2.2)
centromere= c(48,
39, 47, 29, 29, 39, 39, 34, 35, 34, 40, 30, 17, 19, 20, 41, 34, 31, 47, 45, 31,
30, 40, 27)
Figure2.2Top =
function ()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*3
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.1
width=.005
left.right=.111
lines(c(left.left+xoff+.008,left.right+xoff+width+.003),c(mid,mid))
rect(left.right+xoff,bot,left.right+width+xoff,mid,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
color<-c(rep(1,23),0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.02,.45),centre=c(.115,1))
lines(sto)
y<-chrom(RL[24],CI[24])
oldtop=y[3]
draw.chrom(y,xoff=0,color=1)
y<-chrom(RL[23],CI[23])+oldtop+.03
oldtop=y[3]
draw.chrom(y)
to.draw=c(19,16,13,4,1)
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,color[i])
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,abs(color[i]-1))
}
}
Figure2.2Top()
Figure2.2Mid=function()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*3
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.1
width=.005
left.right=.111
lines(c(left.left+xoff,left.right+xoff+width),c(mid,mid))
rect(left.left+xoff,bot,left.left+width+xoff,mid,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,mid,col=color)
rect(left.left+xoff,bot,left.left+width+xoff,top,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
color<-c(rep(1,23),0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.02,.5),centre=c(.11,1))
lines(sto)
y<-chrom(RL[24],CI[24])
oldtop=y[3]
draw.chrom(y,xoff=0,color=1)
y<-chrom(RL[23],CI[23])+oldtop+.03
oldtop=y[3]
draw.chrom(y)
to.draw=c(19,16,13,4,1)
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,color[i])
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,abs(color[i]-1))
}
}
Figure2.2Mid()
Figure
2.3 – Meiosis. This is drawn using a mix of "R" and Powerpoint
©. To use the R scripts you will need to download the package
"ellipse" to, well, draw ellipses.
Rel.Length=
c(8.4, 8, 6.8, 6.3, 6.1, 5.9, 5.4, 4.9, 4.8, 4.6, 4.6, 4.7, 3.7, 3.6, 3.5, 3.4,
3.3, 2.9, 2.7, 2.6, 1.9, 2, 5.1, 2.2)
centromere= c(48,
39, 47, 29, 29, 39, 39, 34, 35, 34, 40, 30, 17, 19, 20, 41, 34, 31, 47, 45, 31,
30, 40, 27)
Figure2.3
=function ()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*7
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.1
width=.005
left.right=.111
# points(.1079+xoff,mid,pch=19)
lines(c(left.left+xoff,left.right+xoff+width),c(mid,mid))
rect(left.left+xoff,bot,left.left+width+xoff,mid,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,mid,col=color)
rect(left.left+xoff,bot,left.left+width+xoff,top,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
#color<-rbinom(22,1,.5)
color<-c(1,0,1,0,0,1,1,0,0,1,0,1,1,0,0,0,1,1,0,1,0,0,0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.035,.5),centre=c(.133,1))
lines(sto)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
draw.chrom(y)
to.draw=c(19,16,13,4,1)
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,color[i])
}
y<-chrom(RL[24],CI[24])
oldtop=0
draw.chrom(y,xoff=.05,color=1)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=.05,abs(color[i]-1))
}
}
Figure2.3()
Figure2.3L=function
()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*7
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.1
width=.005
left.right=.111
# points(.1079+xoff,mid,pch=19)
lines(c(left.left+xoff,left.right+xoff+width),c(mid,mid))
rect(left.left+xoff,bot,left.left+width+xoff,mid,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,mid,col=color)
rect(left.left+xoff,bot,left.left+width+xoff,top,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
#color<-rbinom(22,1,.5)
color<-c(1,0,1,0,0,1,1,0,0,1,0,1,1,0,0,0,1,1,0,1,0,0,0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.02,.5),centre=c(.11,1))
lines(sto)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
draw.chrom(y)
to.draw=c(19,16,13,4,1)
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,color[i])
}
y<-chrom(RL[24],CI[24])
oldtop=0
# draw.chrom(y,xoff=.05,color=1)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
}
Figure2.3L()
Figure2.3R=function ()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*7
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.1
width=.005
left.right=.111
lines(c(left.left+xoff,left.right+xoff+width),c(mid,mid))
rect(left.left+xoff,bot,left.left+width+xoff,mid,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,mid,col=color)
rect(left.left+xoff,bot,left.left+width+xoff,top,col=color)
rect(left.right+xoff,bot,left.right+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
#color<-rbinom(22,1,.5)
color<-c(1,0,1,0,0,1,1,0,0,1,0,1,1,0,0,0,1,1,0,1,0,0,0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.02,.5),centre=c(.158,1))
lines(sto)
to.draw=c(19,16,13,4,1)
y<-chrom(RL[24],CI[24])
oldtop=0
draw.chrom(y,xoff=.05,color=1)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=.05,abs(color[i]-1))
}
}
Figure2.3R()
Figure2.3LL=function ()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*7
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.11-0.005/2
width=.005
left.right=.111
lines(c(.11-1.5*width,.11+1.5*width),c(mid,mid))
#lines(c(left.left+xoff,left.right+xoff+width),c(mid,mid))
rect(left.left+xoff,bot,left.left+width+xoff,mid,col=color)
rect(left.left+xoff,bot,left.left+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
#color<-rbinom(22,1,.5)
color<-c(1,0,1,0,0,1,1,0,0,1,0,1,1,0,0,0,1,1,0,1,0,0,0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.02,.5),centre=c(.11,1))
lines(sto)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
draw.chrom(y)
to.draw=c(19,16,13,4,1)
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,color[i])
}
y<-chrom(RL[24],CI[24])
oldtop=0
# draw.chrom(y,xoff=.05,color=1)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
}
Figure2.3LL()
Figure2.3RR=function ()
{
library(ellipse)
chrom<-function(rl,ci){
rl<-rl*7
bot<-0
mid<-(1-ci)*rl
top<-rl
return(c(bot,mid,top))
}
draw.chrom<-function(y,xoff=0,color=0){
bot<-y[1]
mid<-y[2]
top<-y[3]
left.left=.11-0.005/2
width=.005
left.right=.111
lines(c(.11-1.5*width,.11+1.5*width),c(mid,mid))
rect(left.left+xoff,bot,left.left+width+xoff,mid,col=color)
rect(left.left+xoff,bot,left.left+width+xoff,top,col=color)
}
RL<-Rel.Length
CI<-centromere
color<-c(1,0,1,0,0,1,1,0,0,1,0,1,1,0,0,0,1,1,0,1,0,0,0)
RL<-RL/sum(RL)
CI<-CI/100
plot(c(0.05,.25),c(-.25,2.25),type='n',axes=F,xlab='',ylab='')
sto=ellipse(x=0,scale=c(.02,.5),centre=c(.11,1))
lines(sto)
y<-chrom(RL[24],CI[24])
draw.chrom(y,color=1)
y<-chrom(RL[23],CI[23])
oldtop=y[3]
to.draw=c(19,16,13,4,1)
for(k in 1:5){
i=to.draw[k]
y<-chrom(RL[i],CI[i])+oldtop+.03
oldtop<-y[3]
draw.chrom(y,xoff=0,abs(color[i]-1))
}
}
Figure2.3RR()
Figure 2.5 – Drawing a "cartoon" of a B-DNA
dodecamer (CGCGAATTCGCG)
First
get the data file from the "protein data bank" (http://www.rcsb.org/pdb) - http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BNA
Download
Jmol and install from http://jmol.sourceforge.net/download/
Start
Jmol, go to File/Open/ and open 1BNA.pdb. Right click in the chemical
structure drawing and go through the menu /Style/Structures/Cartoon. Do
this two more times for /Color/Background/White and /Color/Structures/White,
then use the mouse to rotate the structure as you see fit.
Figure 2.8 – Drawing a Robertsonian translocation
karyogram – Open http://www.cydas.org/OnlineAnalysis/WebExample4.aspx
in a different tab or window so that you will have access to both that site and
the instructions here. In the first box replace:
46,y,-7,+8,t(9;22)(q341;q112),i(17)(q10),+der(22)t(9;22)
with:
45<2n>,XY,der(14;21)(q10;q10)
The easiest way to make this replacement is to mark
and copy 46<2n>,XY and then past over the selected text
"46,y,-7,+8,t(9;22)(q341;q112),i(17)(q10),+der(22)t(9;22)"
In the "drawing sequence" box replace:
1,2,3,4,5,6,7,X,8,9,10,11,BR,12,13,14,15,16,17,18,19,20,21,22,Y,?
with:
1,2,3,4,5,6,7,8,BR,9,10,11,12,13,14,15,16,BR,17,18,19,20,21,22,X,Y
In the "Banding resolution" radio buttons
select 800 bands. Uncheck the "color" box if you want it in
black and white. Then click the "Draw" button.