A1.

2 Nucleic Acids Guiding Questions

Sub-Topic Clarification Questions
A1.2.1—DNA as the Some viruses use RNA as their 1. What is DNA and where is it found in cells?
genetic material of all genetic material but viruses are not 2. Are there organisms with genetic material other than DNA?
living organisms considered to be living.
3. How does DNA store genetic information?
4. Label and annotate the structures of this single nucleotide.
In diagrams of nucleotides use
circles, pentagons and rectangles to a.
A1.2.2—Components of
represent relative positions of
a nucleotide b.
phosphates, pentose sugars and
bases.
c.
A1.2.3—Sugar– Sugar–phosphate bonding makes a 5. What is the sugar-phosphate backbone in DNA and RNA?
phosphate bonding and continuous chain of covalently 6. How are the sugar and phosphate molecules connected in the backbone?
the sugar–phosphate bonded atoms in each strand of DNA 7. Draw and annotate the sugar-phosphate backbone of DNA and RNA.
“backbone” of DNA and or RNA nucleotides, which forms a
RNA strong “backbone” in the molecule.
8. How does the arrangement of the sugar-phosphate backbone allow for complementary base pairing in DNA and
A1.2.4—Bases in each
Students should know the names of RNA?
nucleic acid that form
the nitrogenous bases. 9. What are the four nitrogenous bases found in nucleic acids?
the basis of a code
10. How do these nitrogenous bases differ from each other in terms of structure?
A1.2.5—RNA as a Students should be able to draw and 11. What is the structure of an RNA molecule?
polymer formed by recognize diagrams of the structure 12. Illustrate both an RNA nucleotide and an RNA polymer.
condensation of of single nucleotides and RNA 13. What is the role of condensation in the formation of RNA?
nucleotide monomers polymers.
In diagrams of DNA structure, 14. How do the bases pair in DNA and RNA?
A1.2.6—DNA as a students should draw the two 15. What is the significance of complementary base pairing in nucleic acids?
double helix made of strands antiparallel, but are not
two antiparallel strands required to draw the helical shape.
of nucleotides with two Students should show adenine (A)
strands linked by paired with thymine (T), and guanine
hydrogen bonding (G) paired with cytosine (C).
between Students are not required to
complementary base memorize the relative lengths of the
pairs purine and pyrimidine bases, or the
numbers of hydrogen bonds.
Include the number of strands 16. What are the differences between the sugars in DNA and RNA in terms of their structure and functionality?
present, the types of nitrogenous Construct a venn diagram to illustrate the similarities and differences.
bases and the type of pentose sugar.
A1.2.7—Differences Students should be able to sketch
between DNA and RNA the difference between ribose and
deoxyribose. Students should be
familiar with examples of nucleic
acids.
A1.2.8—Role of 17. Why is complementary base pairing important in genetics?
complementary base 18. How does complementary base pairing contribute to DNA replication?
Students should understand that
pairing in allowing 19. How does the fidelity of complementary base pairing contribute to genetic stability?
complementarity is based on
genetic information to
hydrogen bonding
be replicated and
expressed
A1.2.9—Diversity of 20. How many unique DNA sequences are possible using the four DNA bases: adenine (A), cytosine (C), guanine (G),
Explain that diversity by any length
possible DNA base and thymine (T)?
of DNA molecule and any base
sequences and the 21. What does the immense diversity of possible DNA sequences allow for in terms of genetic information?
sequence is possible. Emphasize the
limitless capacity of 22. How does DNA's capacity for information storage enable inheritance across generations?
enormous capacity of DNA for
DNA for storing
storing data with great economy.
information
A1.2.10—Conservation 23. What is the genetic code?
of the genetic code 24. Why is the genetic code’s conservation across diverse organisms significant?
Students are not required to
across all life forms as 25. How does the conservation of the genetic code extend to organisms with significant genetic differences?
memorize any specific examples.
evidence of universal
common ancestry
26. What does "5' to 3'" directionality mean in terms of nucleic acids?
Include 5' to 3' linkages in the
27. How are the 5' and 3’ ends of a nucleic acid strand defined?
A1.2.11—Directionality sugar–phosphate backbone and their
of RNA and DNA AHL significance for replication, 28. How does the directionality of nucleic acid strands impact processes like replication and transcription?
transcription and translation.
Adenine–thymine (A–T) and 29. What are purines and pyrimidines in the context of DNA structure?
A1.2.12—Purine-to- cytosine–guanine (C–G) pairs have 30. Draw a purine and a pyrimidine.
pyrimidine bonding as equal length, so the DNA helix has 31. How does purine-to-pyrimidine bonding contribute to DNA helix stability?
a component of DNA the same three-dimensional
helix stability AHL structure, regardless of the base
sequence.
Limit to a DNA molecule wrapped 32. Sketch and label a nucleosome.
around a core of eight histone 33. Use the Jmol visualization (3D View: 1AOI (rcsb.org)) to:
proteins held together by an a. Identify the two copies of each histone protein. This can be done by locating the tail* of each protein.
additional histone protein attached b. Suggest how the positive charges help to form the nucleosome (with the negatively charged DNA
A1.2.13—Structure of a to linker DNA. Application of skills: molecule).
nucleosome AHL Students are required to use
molecular visualization software to
study the association between the
proteins and DNA within a
nucleosome.
Students should understand how the 34. What organism did Hershey and Chase use for their experiment, and why?
results of the experiment support 35. What was the goal of the Hershey-Chase experiment?
the conclusion that DNA is the 36. What were the results of the Hershey-Chase experiment and how did the results of the experiment support the
A1.2.14—Evidence genetic material. NOS: Students conclusion that DNA is the genetic material?
from the Hershey– should appreciate that technological
Chase experiment for developments can open up new
DNA as the genetic possibilities for experiments. When
material AHL radioisotopes were made available
to scientists as research tools, the
Hershey–Chase experiment became
possible.
NOS: Students should understand 37. Who was Erwin Chargaff, and what was his contribution to our understanding of DNA composition?
A1.2.15—Chargaff’s how the “problem of induction” is 38. What did Chargaff's data reveal about the relative amounts of pyrimidine and purine bases in DNA from
data on the relative addressed by the “certainty of different species?
amounts of pyrimidine falsification”. In this case, Chargaff’s 39. What was the tetranucleotide hypothesis proposed in the context of DNA composition?
and purine bases data falsified the tetranucleotide 40. What specific findings from Chargaff's data contradicted the tetranucleotide hypothesis?
across diverse life hypothesis that there was a
forms AHL repeating sequence of the four
bases in DNA

A1.2 Nucleic Acids Guiding Questions - Key

Sub-Topic Clarification Questions
A1.2.1—DNA as the Some viruses use RNA as 1. What is DNA and where is it found in cells?
genetic material of all their genetic material but a. DNA, or deoxyribonucleic acid, is a molecule that carries the genetic instructions for the development,
 functioning, growth, and reproduction of all living organisms.
b. DNA is primarily found within the nucleus of eukaryotic cells and in the nucleoid region of prokaryotic cells.
viruses are not considered 2. Are there organisms with genetic material other than DNA?
living organisms
to be living. a. While DNA is the primary genetic material, some viruses (non-living) use RNA as their genetic material.
b. Retroviruses, such as HIV, have RNA as their genetic material, and they reverse transcribe their RNA into DNA
upon infecting a host cell.
3. How does DNA store genetic information?
a. DNA stores genetic information in the sequence of its four nitrogenous bases: adenine (A), cytosine (C), guanine
(G), and thymine (T).
b. The specific sequence of these bases in a DNA molecule forms a genetic code that dictates the structure and
function of an organism.
4. Label and annotate the structures of this single nucleotide.
In diagrams of nucleotides
use circles, pentagons and
A1.2.2—Components of rectangles to represent
a nucleotide relative positions of
phosphates, pentose
sugars and bases.

5. What is the sugar-phosphate backbone in DNA and RNA?

a. The sugar-phosphate backbone refers to the repeating structural unit that forms the outer edge of the DNA and
RNA double helix.
b. It consists of alternating sugar molecules (deoxyribose in DNA, ribose in RNA) and phosphate groups.
6. How are the sugar and phosphate molecules connected in the backbone?
a. The sugar and phosphate molecules are connected through a covalent bond known as a phosphodiester bond.
b. A phosphate group attaches to the 3' carbon atom of one sugar molecule and the 5' carbon atom of the
adjacent sugar molecule, creating a continuous chain.
7. Draw and annotate the sugar-phosphate backbone of DNA and RNA.

Sugar–phosphate bonding
A1.2.3—Sugar– makes a continuous chain
phosphate bonding and of covalently bonded atoms
the sugar–phosphate in each strand of DNA or
“backbone” of DNA and RNA nucleotides, which
RNA forms a strong “backbone”
in the molecule.

A1.2.4—Bases in each Students should know the 8. How does the arrangement of the sugar-phosphate backbone allow for complementary base pairing in DNA and RNA?
nucleic acid that form names of the nitrogenous a. The sugar-phosphate backbone provides the structural support for the hydrogen bonding between
the basis of a code bases. complementary nitrogenous bases (adenine with thymine/uracil, guanine with cytosine) in DNA and RNA.
b. This base pairing is the foundation of DNA replication and transcription processes.
9. What are the four nitrogenous bases found in nucleic acids?
a. The four nitrogenous bases are adenine (A), cytosine (C), guanine (G), and thymine (T) in DNA, and uracil (U) in
 RNA (replacing thymine).
10. How do these nitrogenous bases differ from each other in terms of structure?
a. Adenine and guanine are purines, with a double-ring structure, while cytosine, thymine (or uracil in RNA), are
pyrimidines with a single-ring structure.
11. What is the structure of an RNA molecule?
a. An RNA molecule has a single-stranded structure, which can fold into intricate three-dimensional shapes due to
base pairing and interactions between nucleotides.
12. Illustrate both an RNA nucleotide and an RNA polymer.

Students should be able to

A1.2.5—RNA as a
draw and recognize
polymer formed by
diagrams of the structure
condensation of
of single nucleotides and
nucleotide monomers
RNA polymers.

13. What is the role of condensation in the formation of RNA?

a. Condensation, or dehydration synthesis, is the chemical reaction that links nucleotide monomers together to
form a polymer.
b. In this process, a water molecule is removed, and the phosphate group of one nucleotide reacts with the
hydroxyl group on the ribose sugar of another nucleotide, forming a phosphodiester bond.
A1.2.6—DNA as a In diagrams of DNA 14. How do the bases pair in DNA and RNA?
double helix made of structure, students should a. Adenine pairs with thymine (A-T) in DNA through two hydrogen bonds, and with uracil (A-U) in RNA.
two antiparallel strands draw the two strands b. Guanine pairs with cytosine (G-C) through three hydrogen bonds.
of nucleotides with two antiparallel, but are not 15. What is the significance of complementary base pairing in nucleic acids?
strands linked by required to draw the helical a. Complementary base pairing ensures accurate replication and transcription of genetic information.
hydrogen bonding shape. Students should b. It allows for faithful transfer of genetic instructions from one generation to the next and from DNA to RNA.
between show adenine (A) paired
complementary base with thymine (T), and
pairs guanine (G) paired with
cytosine (C). Students are
not required to memorize
the relative lengths of the
purine and pyrimidine
bases, or the numbers of
hydrogen bonds.
16. What are the differences between the sugars in DNA and RNA in terms of their structure and functionality? Construct a
venn diagram to illustrate the similarities and differences.

Include the number of

strands present, the types
of nitrogenous bases and
the type of pentose sugar.
A1.2.7—Differences Students should be able to
between DNA and RNA sketch the difference
between ribose and
deoxyribose. Students
should be familiar with
examples of nucleic acids.
 17. Why is complementary base pairing important in genetics?
a. This pairing is crucial as it ensures accurate replication and expression of genetic information.
18. How does complementary base pairing contribute to DNA replication?
A1.2.8—Role of a. During DNA replication, the two strands of the double helix separate, and each strand serves as a template for
complementary base Students should the synthesis of a new complementary strand.
pairing in allowing understand that b. Complementary base pairing guides the incorporation of nucleotides into the new strand, ensuring the exact
genetic information to complementarity is based duplication of genetic information.
be replicated and on hydrogen bonding 19. How does the fidelity of complementary base pairing contribute to genetic stability?
expressed a. The fidelity of complementary base pairing, maintained by hydrogen bonds, helps prevent errors during DNA
replication and other processes.
b. Proofreading mechanisms, such as DNA polymerase proofreading activity, further enhance accuracy in copying
genetic information.
20. How many unique DNA sequences are possible using the four DNA bases: adenine (A), cytosine (C), guanine (G), and
thymine (T)?
Explain that diversity by a. There are four possible bases at each position in a DNA sequence, so for a sequence of length N, there are 4^N
A1.2.9—Diversity of
any length of DNA
possible DNA base possible unique DNA sequences.
molecule and any base
sequences and the 21. What does the immense diversity of possible DNA sequences allow for in terms of genetic information?
sequence is possible.
limitless capacity of a. The vast number of possible DNA sequences means that DNA can encode an extraordinary amount of genetic
Emphasize the enormous
DNA for storing information, enabling the wide range of traits and functions seen in living organisms.
capacity of DNA for storing
information 22. How does DNA's capacity for information storage enable inheritance across generations?
data with great economy.
a. DNA carries genetic information from parent to offspring, ensuring that traits and characteristics are passed
down through generations.
23. What is the genetic code?
a. The genetic code is a set of rules that specifies how sequences of nucleotides in DNA and RNA correspond to
A1.2.10—Conservation sequences of amino acids in proteins.
of the genetic code Students are not required 24. Why is the genetic code’s conservation across diverse organisms significant?
across all life forms as to memorize any specific a. The conservation of the genetic code among various organisms supports the idea of a shared evolutionary
evidence of universal examples. history and common ancestry.
common ancestry 25. How does the conservation of the genetic code extend to organisms with significant genetic differences?
a. Despite genetic diversity, the fundamental rules of the genetic code remain consistent across all organisms,
from bacteria to plants to animals.
A1.2.11—Directionality 26. What does "5' to 3'" directionality mean in terms of nucleic acids?
of RNA and DNA AHL a. In the 5' to 3' direction, the carbon atoms in the sugar molecules of RNA or DNA are numbered from the fifth to
the third carbon atom.
27. How are the 5' and 3’ ends of a nucleic acid strand defined?
a. The 5' end refers to the end of the strand where the phosphate group of the first nucleotide is attached to the
fifth carbon atom of the sugar molecule.
b. The 3' end refers to the end of the strand where the hydroxyl group (-OH) of the last nucleotide's sugar
Include 5' to 3' linkages in molecule is attached to the third carbon atom.
the sugar–phosphate
28. How does the directionality of nucleic acid strands impact processes like replication, translation, and transcription?
backbone and their
a. The directionality of nucleic acid strands is crucial for processes like DNA replication and transcription.
significance for replication,
transcription and b. These processes occur in a 5' to 3' direction, with the newly synthesized strand being built in the opposite
translation. direction.
i. During DNA replication, the parental DNA strands serve as templates for the synthesis of new
complementary strands.
1. The new strand is synthesized in a 5' to 3' direction, while the parental template strand is read
in a 3' to 5' direction.
ii. During transcription, a DNA template is used to synthesize a complementary RNA strand.
1. The RNA strand is synthesized in a 5' to 3' direction, complementary to the DNA template
strand.
A1.2.12—Purine-to- Adenine–thymine (A–T) and 29. What are purines and pyrimidines in the context of DNA structure?
pyrimidine bonding as cytosine–guanine (C–G) a. Purines (adenine and guanine) and pyrimidines (thymine and cytosine) are two types of nitrogenous bases that
a component of DNA pairs have equal length, so form the building blocks of DNA.
helix stability AHL the DNA helix has the same 30. Draw a purine and a pyrimidine.
three-dimensional
structure, regardless of the
base sequence.
 a.
31. How does purine-to-pyrimidine bonding contribute to DNA helix stability?
a. The complementary base pairing of purines with pyrimidines (adenine with thymine, and guanine with cytosine)
forms hydrogen bonds.
b. This pairing maintains the double-stranded structure of DNA, enhancing its stability by establishing consistent
interactions between the strands.
32. Sketch and label a nucleosome.

Limit to a DNA molecule

wrapped around a core of
eight histone proteins held
a.
together by an additional
histone protein attached to 33. Use the Jmol visualization (3D View: 1AOI (rcsb.org)) to:
A1.2.13—Structure of a linker DNA. Application of a. Identify the two copies of each histone protein. This can be done by locating the tail* of each protein.
nucleosome AHL skills: Students are i. A nucleosome is the basic structural unit of chromatin, consisting of DNA wrapped around histone
required to use molecular proteins.
visualization software to ii. In a nucleosome, there are two copies of each of the four core histone proteins: H2A, H2B, H3, and H4.
study the association iii. These histone proteins form an octamer, with two copies of each histone, H2A, H2B, H3, and H4,
between the proteins and making up the core of the nucleosome.
DNA within a nucleosome. iv. The histone tails extend outward from the core and play a role in regulating chromatin structure and
gene expression.
b. Suggest how the positive charges help to form the nucleosome (with the negatively charged DNA molecule).
i. Histone proteins have many positively charged amino acids, particularly lysine and arginine.
ii. The negatively charged DNA backbone is attracted to these positively charged histone proteins
through electrostatic interactions.
iii. The positive charges on the histones neutralize the negative charges on the DNA, promoting a strong
association between DNA and histones.
iv. This electrostatic attraction facilitates the wrapping of DNA around the histone core, forming a
nucleosome.
A1.2.14—Evidence Students should 34. What organism did Hershey and Chase use for their experiment, and why?
from the Hershey– understand how the results a. They used the T2 bacteriophage (a virus that infects bacteria) because it consists of a protein coat and DNA
Chase experiment for of the experiment support core.
DNA as the genetic the conclusion that DNA is 35. What was the goal of the Hershey-Chase experiment?
material AHL the genetic material. NOS: a. The Hershey-Chase experiment aimed to determine whether DNA or protein is the genetic material that carries
Students should appreciate instructions for inheritance in viruses.
that technological
36. What were the results of the Hershey-Chase experiment and how did the results of the experiment support the
developments can open up
conclusion that DNA is the genetic material?
new possibilities for
experiments. When
a. When the ^35S-labeled protein was used, most of the radioactivity remained in the supernatant, indicating that
radioisotopes were made protein didn't enter the bacteria.
available to scientists as b. When the ^32P-labeled DNA was used, the radioactivity was found within the bacteria, indicating that DNA
 research tools, the entered and carried genetic information.
Hershey–Chase experiment c. The presence of ^32P-labeled DNA inside the bacterial cells demonstrated that the genetic material,
became possible. responsible for directing viral reproduction, was DNA, not protein.
37. Who was Erwin Chargaff, and what was his contribution to our understanding of DNA composition?
NOS: Students should a. Erwin Chargaff was a biochemist who conducted pioneering research on the composition of DNA bases.
understand how the b. His work laid the foundation for understanding the base-pairing rules in DNA.
“problem of induction” is 38. What did Chargaff's data reveal about the relative amounts of pyrimidine and purine bases in DNA from different
A1.2.15—Chargaff’s species?
addressed by the
data on the relative
“certainty of falsification”. a. Chargaff's data showed that the amounts of adenine (A) are approximately equal to thymine (T), and the
amounts of pyrimidine
In this case, Chargaff’s amounts of cytosine (C) are approximately equal to guanine (G), regardless of the species.
and purine bases
data falsified the 39. What was the tetranucleotide hypothesis proposed in the context of DNA composition?
across diverse life
tetranucleotide hypothesis a. The tetranucleotide hypothesis suggested that DNA consisted of a repeating sequence of the four bases
forms AHL
that there was a repeating (adenine, thymine, cytosine, and guanine) in a fixed order.
sequence of the four bases 40. What specific findings from Chargaff's data contradicted the tetranucleotide hypothesis?
in DNA a. Chargaff's data revealed that the ratios of adenine to thymine and cytosine to guanine were not equal,
disproving the idea of a repeating tetranucleotide sequence.