DNA/NUCLEIC ACIDS STUCTURE QUIZ INFO.

& SAMPLE QUESTIONS

BEFORE YOU START STUDYING, PLEASE NOTE: As noted in class, studying for this quiz will be
much easier if you are able to recognize the modular nature of how these structures are constructed (for
e.g., a nucleoside = base + ribose; a nucleotide = a nucleoside + phosphate, etc)!
A. KNOW (BE ABLE TO DRAW) THE STRUCTURES OF :
NH2
O
1. Ribose & 2-deoxyribose (and the prime 4numbering system for the ribose ring): CH
3

Pyrimidine

HN

O
HN

Cytosine (C)
Thymine (T)
(DNA and
(DNA and
some RNA)
some RNA)
2. Bases: adenine; guanine; cytosine; thymine; uracil (including numbering!)
NH2

321N

542
1
21
642
1 1
O
N

yrimidine

7
5

N9
H

Purine

321 421
7
6 321 421
542CH31
5 N 542
HN
HN
N
1
18
21
642
21
642
1 1
1
2
O
N
N
1
N
O4
N

Cytosine (C)
(DNA and
some RNA)

NH2

642
754
1 N 1 542 N
21
875
1
21
421 987
N421
N
321
542

Thymine (T) Purine

Uracil (U)
Adenine (A)
(DNA and
(in RNA) (DNA and RNA)
some RNA)

Uracil (U)
(in RNA)

642542 754
21
HN 1 1 N
875
421
21 N421 N
987
H2 N
321
542
H
1

Guanine (G)
(DNA and RNA)

IMPORTANT HINT: Remember that the tricky structure is cytidine because cytidine = the
NH2
O
nucleoside form
whereas cytosine (MISLEADING)
refers to the free base:
8

421

N
N

N
H

Adenine (A)
(DNA and RNA)

HN
H2 N

vs.
H
Guanine (G)
(DNA and RNA)

Cytosine
(nucleoside)
(base)
3. Nucleosides: guanosine, adenosine, uridine, cytidine (including numbering!)

Guanosine

Adenosine

Cytidine

Uridine

4. Deoxyucleosides: 2-deoxycytidine; 2-deoxythymidine (Note: 2-deoxythymidine is also simply called

thymidine), 2-deoxyadenosine; 2-deoxyguanosine;
Same as nucleosides above, but with an H (instead of OH) on 2 C of ribose!

2-deoxyguanosine

2-deoxyadenosine

2-deoxycytidine

2-deoxythymidine (= thymidine)

5. Nucleotides (and deoxynucleotides):

ia) nucleotide monophosphates (=nucleoside monophosphates): AMP, GMP, CMP, UMP and
ib) deoxynucleotide monophosphates (=deoxynucleoside monophosphates): dAMP, dGMP, dCMP,
dTMP (also just called TMP);
iia) nucleotide diphosphates (=nucleoside diphosphates): ADP, GDP, CDP, UDP and
iib) deoxynucleotide diphosphates (=deoxynucleoside diphosphates): dADP, dGDP, dCDP, dTDP
(also just called TDP);
iiia) nucleotide triphosphates (=nucleoside triphosphates): ATP, GTP, CTP, UTP and
iiib) deoxynucleotide triphosphates (=deoxynucleoside triphosphates): dATP, dGTP, dCTP, dTTP
(also just called TTP);
For examples of questions on these, see sample questions 4-6!
For e.g., the 5-nucleotide monophosphates (NMPs) are:

AMP

GMP

UMP

CMP

And the deoxy-5-nucleotide monophosphates (dNMPs), are:

dAMP

dGMP

dTMP(=TMP)

dCMP

FURTHERMORE: You should also be able to draw the phosphates with a mono/di/tri phosphate group
attached to any hydroxyl group on the ribose as specified in the quiz question, or even more than one
hydroxyl group (including cyclic monophospates with the phosphate connected as indicated by the
numbering), for eg (but be able to draw out the complete structure of the base as well!):

*Note: cyclic AMP (cAMP for short) is an important biochemical second messenger signaling molecule!
FYI (For your interest, i.e. have to be able to put together & draw structure but dont have to
know this fact): Guanosine-tetraphosphate (ppGpp) shown to the left, is a nutritional stress
signal & is a major regulator of stringent control, an adaptive response of bacteria to amino
acid starvation

ALSO NOTE: If no number is given for a mono/di/tri phosphate to indicate the position of attachment of
the phosphate to the sugar, assume that -by default- the structure of a 5 phosphate is required (For eg. If a
quiz question asks you to draw the structure of GTP (guanosine triphosphate), assume that the structure of
5-guanosine triphosphate is what is required)
6. Be able to draw A=U(or A=T) or U=A(or T=A) and GC (or CG!) Watson and Crick base pairs:
NOTE:
1. Unless asked for, please DONT
need to draw the attached ribose
but rather just indicate where it
goes with an R (as shown).
2. You should be able to number
the ring atoms on the bases, as
you may be asked to do this. For
an e.g. of this, see the
U (T) = A base pair to the left!
ALSO NOTE (Memorization hint): As
you can see, the bonds to ribose are on
the same side in all sets of base pairs!!!

Uracil (Thymine)

Adenine

Guanine

Cytosine

Cytosine

Guanine

B. BE ABLE TO INDICATE:
N-glycosidic linkages, phosphate anhydride (=phosphoanhydride) bonds and phosphoester and
phosphodiester linkages (For e.gs of questions on this, see sample Qs 3, 4 & 5)
If the base is a purine or pyrimidine (For e.g.s of questions on this, see sample Qs 1 & 2)
The correct numbering of the ring atoms for bases, nucleosides and nucleotides the correct numbers
for these are indicated with their structures shown earlier! (Note: For examples of questions on
numbering, see sample Questions 1, 2, 3, 6 & 7)
C. BE ABLE TO NAME:
The unusual bases: hypoxanthine, inosine (=hypoxanthine+ribose), and xanthine.
(For e.g.s of questions on this, see sample questions 9 & 10)

hypoxanthine

inosine (=hypoxanthine+ribose)

xanthine

IMPORTANT GENERAL NOTE: The structures you need to know for this SQz (and any SQz for that matter!) may
be drawn differently depending on the language (convention) of Organic Chemistry used to draw them! As long as
the Organic Chemistry used to denote them is correct, any correct Organic Chemistry notation of them is acceptable!
For e.g., all 5 structures of ATP shown below, are correct in Organic Chemistry terms and thus are acceptable! Note:
As you can see from these, the riboses can be drawn with or without Hs (and thus for times sake, not drawing them
is recommended)! The only time the riboses must have Hs drawn on them is when the carbons have been explicitly
written out, as in structure 4 below!

SAMPLE DNA QUIZ QUESTIONS: (The quiz will be ~ 2-4 questions like these)
1.
2.
3.
4.
5.
6.
7.

8.

9.

Draw the structure of 2-deoxythymidine. Correctly number all ring atoms. Is this a purine or pyrimidine ring?
Draw the structure of cytosine. Correctly number all ring atoms. Is this a purine or pyrimidine ring?
Draw the structure of adenosine. Circle the N-glycosidic linkage. Correctly number all ring atoms present!
Draw the structure of 2-deoxyguanosine-5-diphosphate (dGDP). Indicate and label the phosphoester linkage(s)
and phosphoanhydride linkage(s) in the structure.
Draw the structure of 2-deoxyguanosine-5-triphosphate (dGTP). Label any phosphate anhydride bonds.
Draw the structure of 2-deoxycytidine-3-monophosphate (3 dCMP). Number the ring atoms (on both the
ribose & the base) with their proper notation.
Draw a T:A Watson & Crick base pair, with the T on the left and the A on the right (and do not draw it upside
down to skirt this requirement)! Make sure to number all atoms ring atoms on the bases. (Note: You only need
to draw the bases of the base pair and dont need to draw the ribose- instead use an -R to indicate where the
base is connected to ribose)
Draw a G:C Watson & Crick base pair, with the G on the left and the C on the right (and do not draw it upside
down to skirt this requirement)! (Note: You only need to draw the bases of the base pair and DO NOT need to
draw the ribose- instead use an -R (or arrow) to indicate where the base is connected to ribose)
What is the name for the structure show to the left?
Ans:__________

10. What is the name for the structure show below?

Ans:__________
11. What is the name for the structure show below?

Ans:__________

ANSWERS TO SAMPLE DNA QUIZ QUESTIONS: (The quiz will be ~ 2-4 questions like these)
1. Draw the structure of 2-deoxythymidine. Correctly number all ring atoms. Is this a purine or pyrimidine ring?

2. Draw the structure of cytosine. Correctly number all ring atoms. Is this a purine or pyrimidine ring?

3. Draw the structure of adenosine. Circle the N-glycosidic linkage. Correctly number all ring atoms present!

4. Draw the structure of 2-deoxyguanosine-5-diphosphate (dGDP). Indicate and label the phosphoester linkage(s)
and phosphoanhydride linkage(s) in the structure.

5. Draw the structure of 2-deoxyguanosine-5-triphosphate (dGTP). Label any phosphate anhydride bonds.

6. Draw the structure of 2-deoxycytidine-3-monophosphate (3 dCMP). Number the ring atoms (on both the
ribose & the base) with their proper notation.

7. Draw a T:A Watson & Crick base pair, with the T on the left and the A on the right (and do not draw it upside
down to skirt this requirement)! Make sure to number all atoms ring atoms on the bases. (Note: You only need
to draw the bases of the base pair and dont need to draw the ribose- instead use an -R to indicate where the
base is connected to ribose)

8. Draw a G:C Watson & Crick base pair, with the G on the left and the C on the right (and do not draw it upside
down to skirt this requirement)! (Note: You only need to draw the bases of the base pair and DO NOT need to
draw the ribose- instead use an -R (or arrow) to indicate where the base is connected to ribose)

9. What is the name for the structure show to the left?

Ans:_ inosine

10. What is the name for the structure show below?

Ans:__xanthine
11. What is the name for the structure show below?

Ans:_ 3'-5'-cyclic adenosine monophosphate (cAMP)