PLIS IB DP

HL Biology

7 : Nucleic Acids
Student Notes
Name : ________________________________

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 Revised
Covered in lesson
reference Syllabus
Checklist questions

7.1 U1 Nucleosomes help to supercoil the DNA

7.1 U2 DNA structure suggested a mechanism for DNA replication

7.1 U3 DNA polymerases can only add nucleotides to the 3’ end of a primer

DNA replication is continuous on the leading strand and discontinuous on the lagging
7.1 U4
strand

7.1 U5 DNA replication is carried out by a complex system of enzymes

7.1 U6 Some regions of DNA do not code for proteins but have other important functions

Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray

7.1 A1
diffraction
Use of nucleotides containing dideoxyribonucleic acid to stop DNA replication in
7.1 A2
preparation of samples for base sequencing

7.1 A3 Tandem repeats are used in DNA profiling

Analysis of results of the Hershey and Chase experiment providing evidence that DNA
7.1 S1
is the genetic material
Utilisation of molecular visualisation software to analyse the association between
7.1 S2
protein and DNA within a nucleosome
Highly repetitive sequences were once classified as “junk DNA” showing a degree of
TOK confidence that it had no role. To what extent do the labels and categories used in the
pursuit of knowledge affect the knowledge we obtain?
Making careful observations—Rosalind Franklin’s X-ray diffraction provided crucial
NOS
evidence that DNA is a double helix. (1.8)

AIM 6 : Design models to illustrate the stages of DNA replication

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 Revised
Covered in lesson
reference Syllabus
Checklist questions

7.2 U1 Transcription occurs in a 5’ to 3’ direction

7.2 U2 Nucleosomes help to regulate transcription in eukaryotes

7.2 U3 Eukaryotic cells modify mRNA after transcription

7.2 U4 Splicing of mRNA increases the number of different proteins an organism can produce

7.2 U5 Gene expression is regulated by proteins that bind to specific base sequences

7.2 U6 The environment of a cell and of an organism has an impact on gene expression

7.2 A1 The promoter as an example of non-coding DNA with a function

7.2 S1 Analysis of changes in the DNA of methylation patterns

The nature versus nurture debate concerning the relative importance of an individual’s
TOK innate qualities versus those acquired through experiences is still under discussion. Is
it important for science to attempt to answer this question?

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 Revised
Covered in lesson
reference Syllabus
Checklist questions

7.3 U1 Initiation of translation involves assembly of the components that carry out the process

7.3 U2 Synthesis of the polypeptide involves a repeated cycle of events

7.3 U3 Disassembly of the components follows termination of translation

7.3 U4 Free ribosomes synthesise proteins primarily for use within the cell

7.3 U5 Bound ribosomes synthesise proteins primarily for secretion of for use in lysosomes

Translation can occur immediately after transcription in prokaryotes due to the

7.3 U6
absence of a nuclear membrane

7.3 U7 The sequence and number of amino acids in the polypeptide is the primary structure

The secondary structure is the formation of alpha helices and beta pleated sheets
7.3 U8
stabilised by hydrogen bonding
The tertiary structure is the further folding of the polypeptide stabilised by interaction
7.3 U9
between R groups

7.3 U10 The quaternary structure exists in proteins with more than one polypeptide chain

tRNA-activating enzymes illustrate enzyme-substrate specificity and the role of

7.3 A1
phosphorylation

7.3 S1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes

The use of molecular visualisation software to analyse the structure of eukaryotic

7.3 S2
ribosomes and a tRNA molecule

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 7.1. S1 Analysis of results of the Hershey and Chase experiment providing evidence that DNA is the genetic
material.

1. Explain why was sulphur used in one experiment and phosphorus in the other.

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2. Describe what the supernatant is.

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3. In both experiments state what separates into the supernatant and the pellet and explain why.

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4. Explain why most of the radioactive sulphur (35S) was found in the supernatant.
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5. Explain why little of the radioactive phosphorous (32P) was found in the supernatant, i.e. most remained in the pellet.

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Hershey and Chase used a bacteriophage (a virus that infects bacteria) to investigate the chemical nature of genes. The
diagram shows a bacteriophage.

The sulphur in the protein and the phosphorus in the DNA of the bacteriophage were radioactively labelled. The data
obtained after bacterial infection and centrifugation are shown in the table.

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 7.1.A1 Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray diffraction.

When X-rays are directed at a material some is scattered by the material. This scattering is known as diffraction. For
X-ray diffraction to work well the material ideally should be crystallised so that the repeating pattern causes
diffraction to occur in a regular way. DNA cannot be crystallised but the molecules were arranged regularly enough
for the technique to work.

To the image add the following using different colours:

o DNA forms a helix

o Twists every 34 Angstrom (Å)

o 10 bases per twist

o DNA is double stranded

o Phosphates are on the outside

https://undsci.berkeley.edu/images/us101/xray.jpg

Nature of Science: Making careful observations—Rosalind Franklin’s X-ray diffraction provided crucial evidence that
DNA is a double helix. (1.8)

Rosalind Franklin’s careful observation and interpretation of the photographic evidence was crucial to Crick’s
and Watson’s successful discovery of the structure of DNA. Her work and her calculations were shown to Crick
and Watson without her permission and they subsequently published their model before she had an opportunity to
publish her work. Her work is now widely recognised as being as important to the discovery of DNA as Crick and
Watson, but unfortunately, she has never shared in the Nobel prize awarded to Crick and Watson as Nobel prizes
cannot be given posthumously (Franklin died in 1958 aged just 37).

What contribution did the X-ray diffraction conducted by Rosalind Franklin make to our understanding of DNA?

A. It identified DNA as the genetic material.

B. It indicated the helical shape of the molecule.
C. It showed that the DNA of eukaryotes was associated with histone proteins.
D. It showed that replication was a semi-conservative process.
7.1.U2 DNA structure suggested a mechanism for DNA replication
Mechanisms for DNA replication are implied by the presence of complementary base pairing in DNA.
Explain why it is only possible for cytosine to pair with guanine and adenine to pair with thymine.
You may find it helpful to use a diagram.
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It is as a result of the combination of data from a range of investigations that this understanding came about.

Proponent Contribution

Franklin

Chagraff

Watson & Crick

Consequently, DNA structure suggests two mechanisms for DNA replication:

1. Replication occurs via _________________________ base pairing (adenine pairs with thymine, guanine pairs with
cytosine)
2. Replication is bi-directional (proceeds in opposite directions on the two strands) due to the
________________________ nature of the strands

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 7.2 U2 Nucleosomes help to supercoil the DNA.

Use the diagram to explain why prokaryotic DNA is described as being

‘naked’ when compared to eukaryotic DNA.

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https://qph.fs.quoracdn.net/main-qimg-
6eea1244ddb25ceff916d5acfec15fcb

In the space below, draw and label the structure of a simplified nucleosome, including the H1 linker and octamer (which
consists of two copies of four different types of histone proteins).

Nucleosomes both protect DNA and allow it to be packaged, this in turn allows DNA to be supercoiled.

Outline why it is essential to supercoil chromosomes.

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https://ib.bioninja.com.au/_Media/organisation-of-dna_med.jpeg

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 a. Outline how nucleosomes help regulate transcription.

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b. State the part of the cell cycle in which the most DNA would be supercoiled.

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7.1.S2 Utilization of molecular visualization software to analyse the association between protein and DNA within a
nucleosome.

Use the RCSB Protein Bank to read about nucleosomes and examine Jmol images of them.

a. Identify the two copies of each histone protein. This can be done by locating the ‘tail of each protein’.
The tails of the proteins are involved in regulating gene expression.

b. Suggest how the positive charges help to form the nucleosome with the negatively charged DNA molecule.
You may find it useful to add a labelled diagram.

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7.1.U3 DNA polymerases can only add nucleotides to the 3’ end of a primer.

Recap
Label the following diagram, including the carbon numbers.

There are ______ DNA polymerases involved in prokaryotic DNA replication.

Name Function

All three are ___________________ and so have a specific shape. This specific shape is especially important in their
____________ __________.

DNA polymerase I DNA polymerase II DNA polymerase III

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 7.1.U4 DNA replication is continuous on the leading strand and discontinuous on the lagging strand.
7.1.U5 DNA replication is carried out by a complex system of enzymes.

Complete the following table and label the diagram above to describe the enzymes involved in prokaryotic DNA
replication and their functions.

Enzyme Function
DNA Gyrase
(aka topoisomerase)
DNA Helicase

DNA Polymerase III

RNA Primase

DNA Polymerase I

DNA Ligase
Single Strand Binding
Proteins (SSBs)

a. Distinguish between the lead strand and the lagging strand.

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Some biochemists are making a mixture of enzymes for DNA replication in the lab. In each of these cases,
something was missing from the mixture. For each situation, deduce which enzyme was missing and justify your
choice.

a. The DNA produced came out as lots of short sections of DNA, a few hundred base-pairs long, rather
than one continuous strand.
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b. Only the lead strand was replicated.

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c. No DNA was replicated. The original DNA remained untouched.

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What are the functions of DNA primase and DNA polymerase I in DNA replication?

Meselson and Stahl conducted experiments using the isotopes 14N and 15N which showed that DNA replication is semi-
conservative. What would they have observed about the distribution of isotopes in the DNA after one round of replication
if DNA replication was conservative rather than semi-conservative?

A. Only 14N DNA

B. Only 15N DNA
C. All DNA half 14N and half 15N
D. Half the DNA with only 14N and half with only 15N

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7.1.U6 Some regions of DNA do not code for proteins but have other important functions.

Distinguish between coding and non-coding regions of DNA.

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There are five main types of non-coding DNA.

Type Function

https://cdn-
prod.servicemaster.com/-/media/Feature/Term
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rev=038f53aa2dfa4b24b1422169a8b15b64&h
=400&w=600&la=en&hash=A2B41E44056A
4928976A57F42EC86A9A

Mnemonic
STING

7.1.A2 Use of nucleotides containing dideoxyribonucleic acid to stop DNA replication in preparation of
samples for base sequencing.
Identify the following molecules and justify your choices H

H H

HO https://cdn.kastatic.org/ka-perseus-images/64e1ccffde9ce9a25833188b2a07e51693a9f5b8.png
HO
- Image altered HO OH

State how dideoxyribonucleic acid affect DNA replication.

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The Sanger method of sequencing uses dideoxynucleotides with an added group.

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Draw a diagram showing the type of dideoxynucleotide used in the Sanger method of sequencing.

https://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/biology/marketing-assets/sanger-sequencing_steps_process_diagram.png

Sanger developed a method for determining DNA base sequences using terminating nucleotides called dideoxyribonucleotides.
After an incubation period, the DNA samples are run on an electrophoresis gel. Results are shown in the diagram.

What is the base sequence of the original DNA template

strand?

A. A C G C C C G A G T A G C C C A G A T T

B. U G C G G G C U C A U C G G G U C U A A

C. A C G C C C G A G U A G C C C A G A U U

D. T G C G G G C T C A T C G G G T C T A A

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 7.1.A3 Tandem repeats are used in DNA profiling

Tandem repeats are areas of non-coding DNA which repeat.

There are two main types used in DNA profiling:

STR_____________________________________________________
VNTR____________________________________________________

The main difference is one of size. STRs are between 4 and 13 bases long, whereas VNTRs are usually 10 – 100 bases long.
STRs have anywhere between 5 and 200 repeats, whereas VNTRs repeat from between 10 and 1,500 times.

Child

Mother

Father

Sketch what you would expect to see with the above samples when separated using gel electrophoresis.

Base ladder Child Mother Father

1

10

20

Citations:

Allott, Andrew. Biology: Course Companion. S.l.: Oxford UP, 2014. Print.
Taylor, Stephen. "Essential Biology 03.3 07.1 DNA Structure.docx." Web. 1 Oct. 2014.
<http://www.slideshare.net/gurustip/essential-biology-33-71-dna-structure-core-ahl>.
Taylor, Stephen. "Essential Biology 03.4 07.2 DNA Replication.docx." Web. 1 Oct. 2014.
<http://www.slideshare.net/gurustip/essential-biology-34-72-dna-replication-core-ahl>
Bioninja – AHL Pages 7.1

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 7.2.A1 The promoter as an example of non-coding DNA with a function.

Genes are made up of ________ main sections. The promoter and terminator sections are non-coding, but perform
specific functions.

https://ib.bioninja.com.au/higher-level/topic-7-nucleic-
acids/72-transcription-and-gene/sections-of-a-gene.html

Promoters are located upstream / downstream of the gene they are associated with.
It is responsible for the initiation of transcription / translation.
The promoter has a binding site for RNA / DNA polymerase.
In eukaryotes / prokaryotes there are also a number of transcription factors involved.
These factors can either bind near to (proximal / distal) or further from (proximal / distal) the promoter.

7.2.U5 Gene expression is regulated by proteins that bind to specific base sequences in DNA.

Bind to Impact when missing

Transcription factors

Regulatory proteins

Describe and explain the effect of there being a silencer in the

location where an enhancer is shown in the image to the left
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https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/72-transcription-
and-gene/sections-of-a-gene.html

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Complete the table to outline the functions of the different types of gene expression regulation by proteins that occur in
eukaryotes.

DNA Sequence Binding protein Function

Enhancers Activator

Silencers

A region of DNA located close to a specific gene. Once bound to the

sequence RNA polymerase transcribes the gene.

7.2.U6 The environment of a cell and of an organism has an impact on gene expression.

https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/72-transcription- http://www.essaywriterpros.com/environment-controls-gene-expression-sex-
and-gene/sections-of-a-gene.html determination-and-the-onset-of-genetic-disorders/

What is a morphogen?
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What effect do morphogens have?

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https://phys.org/news/2019-07-secrets-
sex-changing-fish-revealed.html
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 7.2.U2 Nucleosomes help to regulate transcription in eukaryotes.

Sketch and label a nucleosome (5 marks)

There are a number of changes which can be made to nucleosomes to either increase or decrease the ease with which the
DNA is transcribed.

Molecule Increase or decrease

What is done? Why?
affected transcription?

DNA

Histone

miRNA

https://www.researchgate.net/figure/Simplified-overview-of-main-epigenetic-modifications-A-
20 Chromosomal-DNA-is-packaged_fig1_333836553
How can environmental factors affect the expression of genes?

A. By promoting the replication of nucleosomes

B. By inactivating epinephrine
C. By making specific changes to the base sequence of genes
D. By causing the pattern of DNA methylation to be changed

Explain the control of gene expression in eukaryotes. (8 marks)

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Outline the structure and functions of nucleosomes. (4 marks)

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 7.2.S1 Analysis of changes in the DNA methylation patterns.

The images show a mapping of chromosomal regions with differential DNA methylation in monozygotic (identical)
twins.

The numbers below each chromosome indicate which four chromosomes, from the twenty three pairs that humans
possess, are being analysed.

The diagrams maps changes between the twins’ levels of methylation of DNA across the chromosomes.

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 a. Compare the diagrams (not the graphs) and summarise the evidence.

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b. Analyse the evidence and deduce conclusions that can be made using DNA methylation.
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Very soon after fertilization, parental epigenetic methylation is reversed in the DNA.
Later, tissue-specific epigenetic modifications are made to the embryonic DNA. The graph follows the degree of
methylation from different sources during embryonic development.

According to the graph, what are the changes in DNA methylation during embryonic development?

A. Only the paternal DNA becomes demethylated.

B. The maternal DNA becomes demethylated first.
C. The methylation patterns of the parents’ DNA are erased before fertilization.
D. The methylation patterns of both parents are erased after fertilization.

Answer Rationale for it NOT being correct

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 7.2.U1 Transcription occurs in a 5’ to 3’ direction.

On the diagram, label the following: DNA, RNA, RNA polymerase, 5’, 3’, RNA nucleotides, 5’ to 3’ direction

https://ib.bioninja.com.au/_Media/tr
anscription-summary_med.jpeg

Use this image to put these steps in the correct order.

http://botanystudies.com/wp-
content/uploads/2017/09/Steps-of-Transcription.jpg

Suggested order Correct order P or O

As RNA polymerase moves along with DNA RNA nucleotides are
added at the 3’ end against the template strand

Transcription factors bind to the promoter which is found upstream

of the coding section of the gene

When the RNA polymerase reaches the terminator, the transcription

factors dissociate and the RNA polymerase also drops off

RNA polymerase binds and unwinds the DNA strands without

separating them

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 7.2.U3 Eukaryotic cells modify mRNA after transcription.

There are three main modifications made to

mRNA in eukaryotes before it leaves the nucleus:

1.

2.

3.

https://www.mun.ca/biology/sc
arr/iGen3_05-12_Figure-L.jpg

7.2.U4 Splicing of mRNA increases the number

of different proteins an organism can produce.

Describe an example of where alternative splicing is of particular benefit to humans.

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 Citations:

Allott, Andrew. Biology: Course Companion. S.l.: Oxford UP, 2014. Print.

Taylor, Stephen. "Essential Biology 7.3 & 7.4 Transcription and Translation (AHL).docx." Web. 1 Oct. 2014.
<http://www.slideshare.net/gurustip/essential-biology7-37-4transcriptiontranslationahl.docx>.

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