Nucleic Acids: Sugars & Bases Biochemistry > Genetic Information > Genetic Information
NUCLEIC ACIDS: SUGARS & BASES
SUMMARY
DNA
• 4 Nitrogenous base (adenine, guanine, cytosine, thymine)
RNA
• Phosphate
• 4 Nitrogenous base (adenine, guanine, cytosine, uracil)
• Ribose
DIFFERENCES BETWEEN DNA AND RNA
• DNA has deoxyribose. RNA has ribose.
• DNA uses thymine. RNA uses uracil
- Whereas ribose has an hydroxyl at carbon 2, deoxyribose does NOT.
PURINES
• Guanine (G)
• Adenine (A)
• Double-ring structure with 4 nitrogens and 4 double bonds.
PYRIMIDINE
1 / 12 • Cytosine (C)
• Thymine (T) DNA only
• Uracil (U) RNA only
• One ring structure with 2 nitrogens and 3 double bonds.
3 hydrogen bonds between G and C
• The amino group hydrogen on C2 of guanine bonds with the carbonyl oxygen on C2 of cytosine
• The hydrogen atom bound to N1 of guanine bonds with N3 of cytosine.
• An amino group hydrogen on C4 of cytosine bonds with the carbonyl oxygen on C6 of guanine.
2 hydrogen bonds between A and T/U
• The hydrogen atom on N3 of thymine/uracil bonds with N1 of adenine
• An amino group hydrogen on C6 of adenine bonds with the carbonyl oxygen on C4 of thymine/uracil
FULL TEXT
Overview Here we will learn about about the structures of the sugars and nitrogenous bases that constitute nucleic acids and about base pairing. NUCLEIC ACIDS
There are two types of nucleic acids:
• DNA (deoxyribose nucleic acid)
• RNA (ribose nucleic acid)
- They are distinguished by the bases and the types of sugars that comprise them.
• Nucleotides are the building blocks of nucleic acids (DNA and RNA).
• Each nucleotide has three components
- Nitrogenous base
- Sugar
- At least one phosphate group.
DNA
2 / 12 • DNA's components are:
- deoxyribose (which is its sugar)
- 1 phosphate
- 4 bases
RNA
• RNA's components are:
- ribose (which is its sugar)
- 1 phosphate
- 4 bases
The 4 Bases of DNA & RNA
• For both DNA and RNA, 3 of the 4 bases are:
- Adenine
- Cytosine
- Guanine
• For DNA, the 4th base is:
- Thymine.
• For RNA, the 4th base is:
- Uracil.
NUCLEOTIDE SUGARS & BASES
Now let's draw the sugars and bases of a nucleotide.
DNA & RNA
We begin with the sugars:
• Deoxyribose (of DNA)
• Ribose (of RNA)
- As we'll see, deoxyribose has one less hydroxyl group than ribose, hence its name deoxy-ribose.
Deoxy-ribose
3 / 12 • To draw deoxyribose, draw a pentagon with an oxygen atom inserted at the top.
- Label carbons 1' through 4' going clockwise from the oxygen atom.
- Now add carbon 5' as an attachment to carbon 4'.
- Next, let's add hydroxyl groups to carbons 1', 3' and 5'.
Ribose
• To draw ribose, draw a pentagon with an oxygen atom inserted at the top.
- Label carbons 1' through 4' going clockwise from the oxygen atom,
- Add carbon 5' as an attachment to carbon 4'.
- Finally, add hydroxyl groups to carbons 1', 2', 3', 5'.
• Specify that whereas ribose has an hydroxyl at carbon 2', deoxyribose does NOT.
NITROGENOUS BASES
Now let's draw the nitrogenous bases.
• There are two general categories of nitrogenous bases in nucleic acids:
- Purines
- For each category, we will first draw their general structures and then the bases that are part of this group.
Purines
• Purines are guanine (G) and adenine (A).
Pyrimidines
• Pyrimidines are cytosine (C), thymine (T) and uracil (U).
PURINE STRUCTURE
• For the general structure of a purine, draw a hexagon.
- Label positions 1 through 6 going counterclockwise starting to the left of the top of the hexagon.
- Insert a nitrogen atom at position 1.
- Then, position 3.
4 / 12 • Now add a double bond between N1 and C6.
- Add another double bond between C2 and N3.
- Add a third double bond between C4 and C5
• Next, at positions 4 and 5 add a second, five-membered ring: it's shaped like a pentagon.
- Now going clockwise from the top of the pentagon, label positions 7, 8 and 9.
• Insert a nitrogen atom at position 7.
- Then, position 9.
• Now add a double bond between N7 and C8.
- Finally, add a hydrogen atom to N9.
THE PURINES
• As we begin to draw the purines, keep in mind that they all have four double bonds: we can use this to check our structures.
Adenine
• Redraw our general purine structure with its 4 double bonds but add an NH2 group to C6.
Guanine
Next, let's draw guanine.
• Redraw the general purine structure, but without the double bonds.
- Add a hydrogen atom to N1.
- Add an NH2 group to C2.
- Add a double-bonded oxygen to C6.
• Now let's add the 3 other double bonds:
- Between C2 and N3
- Between C4 and C5
- Between N7 and C8
THE PYRIMIDINES
Now, let's turn our attention to the pyrimidines.
• For the general structure of a pyrimidine, draw a hexagon.
5 / 12 - You'll notice artificial breaks in the hexagon that we will fill in momentarily.
• Label positions 1 through 6, going counterclockwise, beginning at the bottom of the hexagon.
• Insert a nitrogen atom at position 1
- Then, at position 3
• Now add a double bond between N1 and C2
- Add another double bond between N3 and C4
- Add a third double bond between C5 and C6
• Indicate that the pyrimidine structure is similar to the hexagonal ring of purine.
• As we begin to draw the pyrimidines, keep in mind that they all have three double bonds.: we can use this to check our structures.
Cytosine
• Redraw our general pyrimidine structure without the double bonds.
- Add a hydrogen atom to N1
- Add a double-bonded oxygen to C2
- Add an NH2 group to C4
• Now let's add the 2 other double bonds as follows:
- Between N3 and C4
- Between C5 and C6
Thymine
• Redraw our general pyrimidine structure, but without the double bonds.
- Add a hydrogen atom to N1
- Then, N3.
• Now, add the 3 double bonds:
- Add a double-bonded oxygen to C2
- Then, to C4
• Now add a double bond between C5 and C6
- Next, add a methyl group to C5: We'll see how it makes thymine unique to DNA
• Write that thymine is found in DNA (Not RNA).
6 / 12 Uracil
• Redraw thymine, but omit the methyl group at C5.
- Indicate that it is unique to RNA; it's not found in DNA.
- Specify that the sole difference is that uracil lacks the methyl group, which is found on thymine.
THE DOUBLE-STRANDED STRUCTURE OF DNA
Finally, we will show how the bases can form base pairs with each other to create the double-stranded structure of DNA.
ADENINE AND THYMINE PAIRING
• Write that adenine and thymine pair with each other via hydrogen bonds.
• Show that they pair as follows:
- The hydrogen atom on N3 of thymine bonds with N1 of adenine.
- An amino group hydrogen on C6 of adenine bonds with the carbonyl oxygen on C4 of thymine.
CYTOSINE AND GUANINE PAIRING
• Write that cytosine and guanine pair with each other via hydrogen bonds.
• Show that they pair as follows:
- An amino group hydrogen on C2 of guanine bonds with the carbonyl oxygen on C2 of cytosine.
- The hydrogen atom bound to N1 of guanine bonds with N3 of cytosine.
- An amino group hydrogen on C4 of cytosine bonds with the carbonyl oxygen on C6 of guanine.
CORRECTION REGARDING NUMBERING (PRIMING)
• Please be advised that the final image has been updated to reflect that by standard convention, the carbon atoms of the pentose sugar in nucleotides are designated with a prime ('), thus their numbering is 1', 2', 3', and so forth, whereas the numbering of the carbon atoms in the base does not contain the prime designation.
• Consider that the directionality of DNA strands as being: 5' to 3' or 3' to 5' refers to the carbon atom sugars.
- The prime designation is not yet a part of this video tutorial but will be incorporated into it soon.
FULL-LENGTH TEXT
7 / 12
• Here we will learn about about the sugars and nitrogenous bases that constitute nucleic acids and how they pair at their nitrogenous bases via hydrogen bonds.
• Start a table.
• Denote that there are two types of nucleic acids: DNA and RNA.
• Denote that nucleotides are the building blocks of nucleic acids (of DNA and RNA).
• Denote that each nucleotide has three components: a nitrogenous base, a sugar, and at least one phosphate group. - We will learn the specific names and structures of these later (again, the difference between a nucleoside and a nucleotide is that a nucleoside is just the sugar and base – the nucleotide also includes the phosphate).
• Denote that DNA's components are deoxyribose (which is its sugar), a phosphate, and four bases.
• Denote that RNA's components are ribose (which is its sugar), a phosphate, and four bases.
• Denote that 3 of the 4 Nitrogenous Bases are shared between DNA & RNA, they are: adenine, cytosine, guanine.
- Adenine (A) and guanine (G) are purines: we think of them as being the larger form of nitrogenous bases and we think about their derivation of ATP/GTP (adenine, guanine).
- DNA's 4th base is thymine.
- RNA's 4th base is uracil.
- Thymine (T), uracil (U), and cytosine (C) are pyrimidines: we think of them as being the smaller form of nitrogenous bases we think of their chemistry of UMP (uracil) to dTMP (thymine) & CTP (cytosine).
We'll start with the sugars of a nucleotide and then address the nitrogenous bases.
• Start with the sugars:
- Deoxyribose (of DNA)
- Ribose (of RNA)
• As we'll see, deoxyribose has one less hydroxyl group than ribose, hence its name deoxy-ribose.
8 / 12 • To draw deoxyribose, draw a pentagon with an oxygen atom inserted at the top.
• Label carbons 1' through 4' going clockwise from the oxygen atom.
• Now add carbon 5' as an attachment to carbon 4'.
• Next, let's add hydroxyl groups to carbons 1', 3' and 5'.
• To draw ribose, draw a pentagon with an oxygen atom inserted at the top.
• Label carbons 1' through 4' going clockwise from the oxygen atom,
• Add carbon 5' as an attachment to carbon 4.
• Finally, add hydroxyl groups to carbons 1', 2', 3', 5'.
• Specifically indicate that whereas ribose has an hydroxyl at carbon 2', deoxyribose does NOT.
Now let's draw the nitrogenous bases.
• For the general structure of a purine, draw a hexagon.
• Label positions 1 through 6 going counterclockwise starting to the left of the top of the hexagon.
• Insert a nitrogen atoms at positions 1 and 3.
• Now add double bonds between N1 and C6, C2 and N3, C4 and C5.
• Next, add a five-membered ring, shaped like a pentagon.
9 / 12 • Now going clockwise from the top of the pentagon, label positions 7, 8 and 9.
• Insert nitrogen atoms at positions 7 and 9.
• Now add a double bond between N7 and C8.
• Finally, add a hydrogen atom to N9.
As we begin to draw the purines, keep in mind that they all have four double bonds. We can use this to check our structures.
Now that we have the general structure, let's draw adenine.
• Redraw our general purine structure with its 4 double bonds but add an NH2 group to C6.
- In the purine biosynthesis tutorial, we learn that adenylosuccinate synthetase catalyzes the addition of the amine group from via aspartate addition via GTP phosphorylation.
Next, let's draw guanine.
• Redraw the general purine structure, but without the double bonds.
• Add a hydrogen atom to N1.
• Now let's add the 3 other double bonds between:
- C2 and N3
- C4 and C5
- N7 and C8.
• Add an NH2 group to C2.
• The amine group is added via ammonia produced from glutamine hydrolysis in the process of inosinate (IMP) conversion to GMP.
• Add a double-bonded oxygen to C6.
10 / 12 • Also, add an oxygen doubled-bonded to C6, since guanine derives from inosinate, which is oxygenated at C6 (again we learn about inosinate and its conversion to guanine in our purine biosynthesis tutorial).
Now, let's turn our attention to the pyrimidines.
• For the general structure of a pyrimidine, draw a hexagon (you'll notice artificial breaks in the hexagon that we will fill in momentarily).
• Label positions 1 through 6, going counterclockwise, beginning at the bottom of the hexagon.
• Insert a nitrogen atom at position 1
• Then, at position 3.
• Now add double bonds between N1 and C2, N3 and C4, C5 and C6.
• Indicate that the pyrimidine structure is similar to the hexagonal ring of purine.
As we begin to draw the pyrimidines, keep in mind that they all have three double bonds. This will help us to double- check our structures for accuracy.
Now, the pyrimidines.
First, uracil, the sole nucleic acid found in RNA, only.
• Draw the standard pyrimidine ring.
• Then, include double-bonded oxygens at carbons 2 and 4 (they are found in orotate (the building block of uracil, which we learn about in the pyrimidine biosynthesis tutorial).
- Specifically show that the sole difference is that uracil lacks a methyl group at C5', which is found on thymine.
Now, thymine the sole nucleic acid found in DNA, only.
• Draw the standard pyrimidine ring.
• Add a methyl at carbon 5' (which differentiates it from uracil (its RNA counterpart).
11 / 12 • Then, again, include the double-bonded oxygens at carbons 2 and 4 (they are found in orotate (the building block of thymine, which we learn about in the pyrimidine biosynthesis tutorial).
Now, cytosine:
• Again, draw the pyrimidine ring.
• Add a double-bonded oxygen to C2 (it was found in orotate at carbon 2).
• BUT at carbon 4, add an amino group, instead (in the pyrimidine biosynthesis tutorial, we learn that that via glutamine hydrolysis, ammonia is added to convert UTP to CTP (via CTP synthetase).
Finally, we will show how the bases can form base pairs with each other to create the double-stranded structure of DNA.
• Adenine & Thymine Pairing
- TWO Hydrogen Bonds.
• Show that:
- The hydrogen atom on N3 of thymine bonds with N1 of adenine.
- The carbonyl oxygen on C4 of thymine bonds with an amino group hydrogen on C6 of adenine.
• Cytosine and Guanine Pairing
- THREE Hydrogren Bonds.
• Show that:
- The carbonyl oxygen on C2 of cytosine bonds with an amino group hydrogen on C2 of guanine.
- N3 of cytosine bonds with the hydrogen atom bound to N1 of guanine.
- An amino group hydrogen on C4 of cytosine bonds with the carbonyl oxygen on C6 of guanine.
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