CLASS: FUNDAMENTALS I
DATE: Tuesday, September 14, 2010, 10-11am
PROFESSOR: DR. CHEN
LECTURE TITLE
Scribe: PEYTON YARBROUGH
Proof: CALVIN SIMS
Page 1 of 5
I. Lectures Cover [S1]
II. Chapter 10 – Nucleotides and Nucleic Acids [S2]
III. Nucleotides and Nucleic Acids [S3]
a. All nucleotides and nucleic acids are biological molecules that posses heterocyclic nitrogenous bases. I will
show you what nucleotide is.
b. Nucleic acid is a polymer of a nucleotide. So that means nucleotides are linked together to form a very long
polymer so that’s a nucleic acid.
c. Nucleic acid important to store your genetic information and then transfer that genetic information to the
protein and then the protein is mainly doing the biological process in your cells.
d. There are two kinds of nucleic acids
i. DNA – already covered that part.
ii. RNA – serve in the expression of genetic information stored in DNA. I will mention this in more detail later.
Through the process of transcription and translation. Transcription is the process in which to make RNA.
That’s what you want to pass your genetic information to a protein. To make a protein that process is
called translation.
e. We are not covering today transcription but not translation either so we are covering what is RNA first and
then also there is a regulation between transcription and before translation. And then that regulation we call
post-transcriptional regulation.
IV. Importance of DNA and RNA [S4]
a. The importance of DNA and RNA is that genetic information is stored in the DNA.
b. Information encoded in a DNA molecule is transcribed to an RNA. So that’s called transcription.
c. The sequence of RNA will be read and is translated into protein or into a sequence of amino acids. That’s
called a translation.
V. Information Transfer in Cells [S5]
a. Here I show you that the genetic information is stored in the DNA and the DNA can be replicated by yourself.
Then you can pass the genetic information into the daughter cells.
b. The genetic information stored in the DNA needs to be translated into the protein.
c. The protein is doing the most function in your body in your cells.
d. There’s no direct transfer from the DNA to the protein. So in other words, DNA cannot directly translate into
the protein.
e. Cells use intermediate molecule such as we call that RNA so the DNA is transcribed to the RNA and the
RNA is translated into the protein.
f. Again defines transcription and translation.
g. In between transcription and translation there is post-transcription regulation.
VI. What Constitutes a Nucleotide (Nucleic Acid)? [S6]
a. If you take a nucleotide or nucleic acid and then you hydrolyze a nucleotide you would get three things in
equal amounts:
i. first one is nitrogenous base.
ii. Second one is five-carbon sugar.
iii. Third would be phosphoric acid.
b. These three things constitute a nucleotide.
VII. Nitrogenous Base [S7]
a. There are two kinds of nitrogenous bases
i. one is called pyrimidines. Six membered aromatic ring containing two nitrogens I will show you in the next
slide. Two pyrimidines are found in RNA: cytosine and uracil.
ii. The second is called purine. It looks similar to pyrimidines but it is composed of two rings. One resembles
pyrimidine ring and the other resembles imidazole ring. Two purines are found in both RNA and DNA:
adenine and guanine.
VIII. Figure 10.2 [S8]
a. Here shows you the structure of the pyrimidine ring and the purine ring.
b. Points out the nitrogens and how you number them but then says you don’t need to know how they are
numbered.
c. Points out rings and numbers of purine ring system but again says you don’t have to memorize numbering
system.
IX. Figure 10.3 [S9]
a. Three pyrimidines. Two are found in RNA and two are found in DNA.
b. Those found in RNA is cytosine and uracil.
c. Those found in DNA is cytosine and thymine.
CLASS: FUNDAMENTALS I
Scribe: PEYTON YARBROUGH
DATE: Tuesday, September 14, 2010, 10-11am
Proof: CALVIN SIMS
PROFESSOR: DR. CHEN
LECTURE TITLE
Page 2 of 5
d. Don’t have to know the structures. He can’t remember the structures either.
X. Figure 10.4 [S10]
a. Here are the two purines, adenine and guanine found in the DNA and RNA.
b. They are two rings.
XI. The Sugar (Ribose) [S11]
a. Those are the nitrogenous bases and the next one will be the sugar.
b. Sugar is a ribose actually called a pentose, a five-carbon sugar.
c. The ribonucleoside is called D-ribose but this d-ribose will form a five-membered ring known as furanose and
then those found in the ribonucleoside we called D-ribofuranose. There is a difference in the sugar found in
the DNA and the RNA.
d. The sugar found in the DNA is called deoxyribonucleoside and is called 2-deoxy-D-ribose and also forms a
five-membered ring structure but the C2 position is hydrogen with the absence of oxygen.
e. You remember atoms are 1’,2’,3’ in order to distinguish the atoms found in purines and pyrimidines. Here
you name it 1’, 2’, … ok?
XII. Figure 10.9 [S12]
a. Here is show you the structure of D-ribose which is found in RNA. It will form a five-membered ring structure
and at C2’ position the ribose is containing a –OH group so we know this is the ribose found in the RNA.
b. The ribose found in DNA has no oxygen so it’s hydrogen so that you call D-2-Deoxyribose.
c. So that’s the difference between the ribose in RNA and DNA.
XIII. What is Nucleoside? [S13]
a. So then you have a nitrogen base and you have a sugar. If you put these two things together we call it
nucleoside.
b. The nucleoside found in RNA so there are four different nucleosides right?
c. The nitrogen base is linked to the ribose via glycosidic bond. I will show you what that is.
d. The way you name the nucleoside is you add –osine to the root name of a purine and –idine to the root name
of a pyrimidine.
e. Examples listed on slide.
XIV.
Figure 10.10 [S14]
a. The nitrogenous base which in here is pyrimidine linked to a ribose and you know this is found in RNA
because the C2’ position contains an –OH group and there’s a link there together, a glycosidic bond.
b. And this bottom one is a purine with two rings connected to a ribose.
XV. Figure 10.11 [S15]
a. cytidine and uridine are derived from pyrimidine because you can see the one ring. So this is cytidine fused
to ribose and this is uridine fused to ribose found in RNA.
b. Two purines in RNA, adenonine fused to ribose called adenosine and guanine fused to ribose called
guanosine.
c. So there are four different nucleosides in RNA.
XVI.
SLIDE 16 [S16]
a. The main part of this lecture what is a nucleotide? It is a nucleoside plus a phosphate.
b. Nucleoside binds to a phosphate and is referred to as a nucleotide.
c. The phosphate is esterified to a sugar’s OH group.
d. C-5’ –OH group is esterified with phosphate and those are found in the cells so that in such a way a
ribonucleotide has a 5’ phosphate.
e. So a phosphate is found at the C-5’ and can be from 1-3 phosphates.
XVII. Figure 10.13 [S17]
a. Points out the C5’ position where phosphate is connected in different examples.
XVIII. Figure 10.15 [S18]
a. The phosphate that connects to the C5’ position can also be 2 or 3 phosphates.
b. Here is a phosphate connected to adenosine 5’-monophosphate and it becomes adenosine 5’-diphosphate.
c. So if you add another phosphate to the ADP it becomes ATP.
XIX.
Base, Nucleoside, Nucleotide [S19]
a. in summary this is how we name base, how we name nucleoside, and how we name nucleotide.
XX. What is Nucleic Acid? [S20]
a. We know nucleic acid is a polymer of nucleotides so you fuse many many nucleotides together and it
becomes a nucleic acid.
b. You link them together through 3’ to 5’ phosphodiester bonds. I will show you this in a later slide.
c. It is found that the next 5’ monophosphate is linked to the previous nucleoside fused to the 3’ –OH group.
d. The polymer of ribonucleotides is called RNA>
CLASS: FUNDAMENTALS I
Scribe: PEYTON YARBROUGH
DATE: Tuesday, September 14, 2010, 10-11am
Proof: CALVIN SIMS
PROFESSOR: DR. CHEN
LECTURE TITLE
Page 3 of 5
e. The conventional way to read and write the polynucleotide chain is from the 5’ end to the 3’ end. So you read
your RNA or DNA sequence from 5’ to 3’ according to the nitrogen base.
f. However, the reading from 5’ to 3’ actually passes through each phosphodiester from 3’ to 5’.
XXI.
Figure 10.17 [S21]
a. This is illustrated here.
b. This is a polymer of a nucleotide. This is RNA because we know that C2’ position is –OH group so we know
this is RNA.
c. You read the RNA sequence from 5’ here because C5’ position is here alright?
d. C3’ position is here. So you read from 5’ to 3’.
e. According to the nitrogen base so you read A-C-G-U. You know that A-C-G-U. So the first nucleotide is
adenine. Because you read from 5’ to 3’ and then look here. This is phosphodiester bond. So this
phosphate is fused to C3’ position. And then this phosphate is fused to the C5’ position of the next
nucleotide. So it’s opposite from the reading of nucleic acid. So if you read from 5’ to 3’ but phosphodiester
bond passes from 3’ to 5’. You kind of have to remember this.
f. In the last slide it’s important to remember when there’s ribonucleus to cleave on RNA.
XXII. Figure 10.18 [S22]
a. If someone asks you to draw a sequence of RNA, to be very accurate you have to draw like this but how can
we remember all these structure right? So then a simplified way to represent this sequence. So then since a
sugar and a phosphate are all identical. So you actually don’t need to draw that structure so you can use this
vertical line to represent a ribose alright?
b. Use the slash to represent a phosphodiester bond.
c. Everything is identical. You can omit the phosphate because all phosphate is always there right? So now
you can draw like this but the only thing indicating your nitrogenous base are these letters right?
d. Even more simplified is the TCGAT where you only put the nitrogenous base but you can recall what it looks
like.
e. Is this DNA or RNA? This is DNA because you have thymine, which isn’t present in RNA.
XXIII. What Are the Different Classes of Nucleic Acids? [S23]
a. Two kinds of nucleic acids:
i. DNA – only one type, only serves one purpose, which is storing your genetic information.
ii. RNA – there are 4 different types and they serve different purposes
1. The first one is the focus of our lecture, which is called messenger RNA or mRNA.
2. The second one is called ribosomal RNA or rRNA.
3. The third one is transfer RNA or tRNA.
4. In addition to these RNA there are small nuclear RNA or snRNA, which is very short. And then
snRNA is important for pre-mRNA splicing.
5. Small non-coding RNA is important for post-transcriptional regulation.
XXIV. Table 10.2 – Principle Kinds of RNA Found in an E. coli cell [S24]
a. So if you isolate RNA from the cells for example here if you isolate RNA from E. coli the majority of RNA will
be rRNA, which consists of about 82%.
b. The next would be tRNA.
c. But the least abundant one would be the mRNA. However, the mRNA is maybe the most important because
the mRNA will encode or be translating into the protein.
XXV. Messenger RNA (mRNA) [S25]
a. What are the purpose of different RNA. First one is Messenger RNA but it only consists of about 2%.
b. It’s purpose is to carry information that is encoded in the DNA so you should note that you have genes stored
in the DNA and then you have to encode these genes so you need to transcribe this gene into RNA and that
RNA we call mRNA.
c. Eventually, the mRNA will be translated into a protein.
d. There are a few differences between prokaryotic mRNA and eukaryotic mRNA.
i. Usually a single prokaryotic mRNA can synthesize several proteins or 2 or 3 proteins. One mRNA can
translate into 3 similar function proteins.
ii. In eukaryotic cells one mRNA encodes one protein. However, the subject of eukaryotic mRNA is
compressed and composed of introns and exons.
XXVI. Eukaryotic mRNA [S26]
a. DNA is transcribed into RNA but usually its transcribed into non-mature RNA or pre-cursor mRNA. So we call
pre-cursor mRNA, which means it’s not mature and cannot transcribe because it contains introns and exons.
b. Intron – intervening sequence; cannot translate into the protein.
c. Exon – coding sequence; can translate into protein.
d. The process to remove introns is called splicing.
CLASS: FUNDAMENTALS I
Scribe: PEYTON YARBROUGH
DATE: Tuesday, September 14, 2010, 10-11am
Proof: CALVIN SIMS
PROFESSOR: DR. CHEN
LECTURE TITLE
Page 4 of 5
e. So that’s messenger RNA we know it’s more compressed in the eukaryotic cells. It will be processed into the
mature RNA and that will be translated into protein so that’s the main purpose of mRNA, which is encoding
the genetic information into protein.
f. There is RNA that helps in the translation of RNA. There are two that are important to help the translation of
mRNA. One is rRNA.
XXVII. Ribosomal RNA (rRNA) [S27]
a. rRNA is composed of two parts. One part is RNA the second part is protein. 2/3 of ribosome is RNA and 1/3
is protein. So it is a RNA-protein complex.
b. Ribosome is one to translate mRNA into protein. The role of rRNA is to serve as a scaffold to help the
formation of the ribosome.
c. rRNA forms a very complex secondary structure.
d. The relative size of rRNA you can refer to as sedimentation coefficients or S.
XXVIII. Secondary Structure of rRNA [S28]
a. I will show you here the secondary structure of rRNA. As you can see it’s a very complicated structure.
XXIX. Figure 10.25 – The Organization and Composition of Prokaryotic and Eukaryotic Ribosomes [S29]
a. Here are the ribosomes found in the eukaryotic cells here and found in the prokaryotic cells. You don’t have
to remember the structure I will just give you an idea.
b. They are both made of two subunits. Points out numbers and size of each subunit.
c. One is 40S and one is 60S. so 40S subunit put together with 60S you form an 80S. So that’s the size of a
ribosome.
d. If you look at 40S it contains 18S RNA and contains 33 different proteins.
e. For the 60S you have 28S and 49 proteins. So that’s the ribosome structure. It contains RNA and protein.
f. The purpose of ribosome is to translate protein from mRNA.
XXX. Transfer RNA (tRNA) [S30]
a. So in addition to rRNA there is another subset of RNA, which is called tRNA, which also helps in the
translation of mRNA. Usually tRNA is very small. It’s about 73 to 94 residues. So at most 94 different
nucleotides so it’s very small.
b. They also form into a secondary structure.
c. The purpose of transfer RNA is to carry amino acid to the ribosome and then translate into mRNA into a
protein. Protein contains a whole bunch of amino acids.
d. Each amino acid has at least one unique tRNA.
e. Usually 3’-terminal sequence of tRNA is CCA. The amino acid is linked to this transfer RNA. tRNA brings the
amino acid to the ribosome to translate it. An mRNA to a protein.
XXXI. Secondary Structure of tRNA [S31]
a. So here is just the secondary structure of tRNA. Amino acid is linked to 3’ position.
XXXII. DNA & RNA Differences? [S32]
a. We know that the difference between DNA and RNA is that when the C2 position contains –OH or –H. If it
contains –OH we know its RNA. So why does DNA contain no –OH group and RNA contains –OH group?
b. They have many reasons. One major reason is that the –OH group found in RNA is very susceptible to
hydrolysis.
c. However, because DNA lacks –OH and is more stable.
d. The genetic material in DNA must be more stable. If it’s unstable the information will be broken or degraded
and then you have mutation and you lose genetic information.
e. Remember, RNA is designed to be expressed for a little while and as long as it expresses a protein it can be
shut down. That is why RNA is very unstable and DNA is very stable.
XXXIII. Hydrolysis of Nucleic Acid [S33]
a. We also know that RNA is very easily hydrolated(?) by dilute base. So if you incubate RNA in alkaline
conditions the RNA will be hydrolyzed but not DNA.
b. DNA and RNA are hydrolyzed by the nucleases. The nucleases are protein or enzymes that can degrade
RNA or DNA. It will be RNAase or DNAase.
XXXIV. Figure 10.29 [S34]
a. So this slide shows you why RNA is very unstable. The slide is not very clear.
b. The C2’ position of RNA contains –OH group so if you incubate RNA with alkaline solution. Alkaline solution
contains –OH right? So the –OH attacks the –OH group and then now you incubate the –OH group and it
becomes, the oxygen is activated right? Because the activation of this oxygen will attach this phosphate
group. The cleavage of this diester bond here. Remember this is 5’ right? So this is C5’. It will cleave at C5’
position. So you cleave here. Once this phosphodiester bond is cleaved a new form of 3’ cyclic phosphate
and this cyclic phosphate is very unstable and will be hydrolyzed easily by the water and it can be easily
broken at this position. Now phosphate is fused to here or it can be broken in here. Now the phosphate is
CLASS: FUNDAMENTALS I
Scribe: PEYTON YARBROUGH
DATE: Tuesday, September 14, 2010, 10-11am
Proof: CALVIN SIMS
PROFESSOR: DR. CHEN
LECTURE TITLE
Page 5 of 5
fused to the 5’. That’s why RNA is very unstable so if you incubate RNA with alkaline base you hydrolyze
RNA into pieces or different nucleotides.
XXXV. Nucleases [S35]
a. The one that hydrolyzes RNA we call RNase. It only hydrolyzes RNA but not DNA.
b. Normally nucleases are phosphodiesterase, which means that these will only hydrolyze phosphodiester
bonds by using water as an attacking group.
c. Remember this, cleavage can occur at either side at either 3’ side or 5’ side. You have to remember which
side is 3’ side or which side is 5’ side. If it’s cleaved at 3’ side then we call it “a”. Cleaved at “a” position
means it’s cleaved at 3” side. If the enzyme is cleaved at the 5’ side then you call it “b”. Next slide I will give
you a structure.
d. The enzyme can either cleave DNA or RNA in the middle. If it cleaves in the middle we call is endo-nuclease.
There are also enzymes that cleave from the outside and we call them exo-nuclease.
e. Know what is endo, what is exo, what is the enzyme cleaved at 3’ position then what kind of nucleotide you
would get after the cleavage.
f. Two examples.
XXXVI. Figure 10.30 [S36]
a. This is the first nucleotide so this is C3’ position. You read the sequence from 5’ to 3’ but this is 3’. This is 5’.
If it’s “a” that means it’s cleaved here. Then when the phosphate is attached after cleavage at “a” the
phosphate attaches to the C5’ right? It cleaves it here. So the phosphate is fused to the C5’ alright?
However, if it’s “b” which means it cleaves at 5’ position here the phosphate will attach to 3’ ok?
b. Summed up on left of the slide: a cleavage yields 5’ phosphate products, whereas b cleavage gives 3’phosphate products.
c. Try to remember what kind of product you would get (where the phosphate attached to: 3’ or 5’?)
XXXVII. Figure 10.31 [S37]
a. Snake venom cleaves from the outside one-by-one at “a”. The product you would get would be 5’
monophosphate. You get 5’ adenosine monophosphate you have the remember this.
b. Spleen phosphodiesterase cleaves “b” position. What kind of product you would get? 3’ cyclic(could be
cystidine?) mono-phosphate
c. Two different products you will get depending on what enzyme you use to hydrolyze your RNA.
XXXVIII.
Table 10.4 – Specificity of Various Nucleases [S38]
a. Only remember the one in the red box. It’s called RNase A found in the pancreas. We know that it’s endonuclease. It cleaves in the middle of your RNA. It cleaves at “b” position but somehow it can recognize the
sequence. So it won’t cleave at every “b” but only after a pyrimidine. If it’s a purine it won’t cleave.
XXXIX. Figure 10.32 [S39]
a. Another example. He cannot read it. Pancreatic RNase A: an endo ribonuclease cleaves “b” after
pyrimidines only at C or U at “b” position. It cleaves at “b” at 3’ pyrimidines. This is what you get if you
incubate RNA with RNase found in the pancreas.
b. We will take 10 minute break and come back.
[End 47:13 mins]