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DNA Notes
3.3 DNA structure
3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate (2)
A DNA nucleotide has a deoxyribose (pentose) sugar covalently bonded to a nitrous base and
phosphate group
3.3.2 State the names of the four bases in DNA (1)
The four bases in DNA are:
1. Adenine
2. Cytosine
3. Guanine
4. Thymine
3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand (2)
The DNA nucleotides are linked together by covalent bonds (phosphodiester bonds) between the
sugars of one nucleotide to the phosphate group of another.
3.3.4 Explain how a DNA double helix is formed (3)
DNA is made of two strands of nucleotides
Nucleotides joined to each other via covalent bonding
The two nucleotide strands are connected together via hydrogen bonds
Nucleotide bases join in a specific pattern; adenine with thymine, cytosine with guanine
Known as complementary base pairing
2 H-bonds between A and T, 3 H-bonds between C and G
3.3.5 Draw an label a simple diagram of the molecular structure of DNA (1)








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3.4 DNA replication
3.4.1 Explain DNA replication (3)
Double helix unzipped and unwound by enzyme DNA helicase (by breaking H-bonds
between base pairs)
This occurs at the replication fork
Results in two parent strands (strands are separated by helicase)
Free nucleotides in the nucleus pair with the parent strands through complementary base
pairing
Joined together via covalent phosphodiester bonds by DNA polymerase
Double strand reforms into double helix via enzyme
Now have two daughter strands identical to the original strands
3.4.2 Explain the significance of complementary base pairing in the conservation of the base
sequence of DNA (3)
Complementary base pairing ensures that A always pairs with T and C with G
Allows DNA to be copied exactly from each generation to the next conservation of base
sequence of DNA
Prokaryotes allows entire genome to be copied into each generation
Eukaryotes all cells retain exact copy of total genome
3.4.3 State that DNA replication is semi-conservative (1)
DNA replication is semi-conservative

3.5 DNA transcription and translation
3.5.1 Compare the structure of RNA and DNA (3)
DNA RNA
Deoxyribose sugar Ribose sugar
Bases A,C,T,G Bases A,C,U,G
2 polynucleotide strands 1 polynucleotide strand


3.5.2 Outline DNA transcription in terms of formation of complementary RNA strand (2)
1. DNA helix is opened at position of gene
2. Helix unwound by RNA polymerase
3. One of the polynucleotide chains acts as a template strand for mRNA
4. Free RNA nucleotides form complementary strand to DNA through base pairing
5. Phosphodiester bonds on RNA strand formed by RNA polymerase
6. Thymine is replaced by Uracil
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7. After mRNA is complete the molecule detaches from DNA and leaves nucleus for
cytoplasmic ribosomes
8. DNA helix reforms

3.5.3 Describe the genetic code in terms of codons composed of triplets of bases (2)
Genetic code consists of 4 bases A, T, C, G
A triplet is used to describe group of 3 bases in DNA
A codon is a group of 3 bases in mRNA
Each codon codes for a particular amino acid
There are 64 codons and 20 amino acids
Therefore codons are degenerate (more than 1 codon for a particular amino acid)
Includes 1 start codon (AUG) and 3 stop codons (UGA/UAA/UAG)
Genetic code is universal













3.5.4 Explain the process of translation, leading to polypeptide formation (3)
Translation is process through which proteins are synthesized
Uses ribosomes, mRNA and tRNA

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1. mRNA is sent out of nucleus to cytoplasm ribosome (composed of rRNA to catalyse reactions)
2. mRNA binds to the small subunit of the ribosome
3. Ribosome moves along the mRNA strand, beginning translation from the start codon (AUG)
4. tRNA (single strand of RNA folded in a particular way, with an acid attachment side and an
anti-codon side) contains anticodons (groups of 3 bases) which are complementary to the
codons on mRNA
5. tRNA will collect the amino acid which corresponds with its anticodon base pairs
6. Then, tRNA binds to the ribosome where its anticodon matches the codon on the mRNA
done through complementary base pairing and form a hydrogen bond
7. 2 tRNA molecules can bind at once.
8. The 2 amino acids carried by the tRNA form a peptide bond
9. The first tRNA then detaches from the ribosome and the second one takes its place the
ribosome moves along the mRNA to the next codon so another tRNA can bind.
10. Process continues until a polypeptide chain is formed.

3.5.5 Discuss the relationship between one gene and one polypeptide (3)
Initially, it was assumed that one gene would code for one polypeptide
Now discovered that the genetic code is universal same bases/codons code for the same
amino acids in all living organisms
Genetic code is degenerate there are 64 codons but only 20 amino acids.
Same amino acid may be coded for by more than 1 codon
Some proteins are composed of a number of polypeptides therefore each polypeptide has
its own gene (e.g. haemoglobin, with 4 polypeptides)
Exceptions:
1. Some genes code or types of RNA which dont produce polypeptides
2. Some genes control the expression of other genes

7.1 DNA structure (HL)
7.1.1 Describe the structure of DNA (2)
DNA has a double helix shape with a uniform diameter along its entire length
Both helices are right-handed
Strand backbones are closer together on one side of the helix called minor groove. Vice
versa = major groove.
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Phosphate group attached to 5 end of the deoxyribose sugar and hydroxyl (OH) group
attached to 3
Two polynucleotide strands are anti-parallel one strand runs 5 to 3, the other runs 3 to 5
Hydrogen bonding between base pairs purines (A and C) bond to pyramidines (G and T)

7.1.2 Outline the structure of nucleosomes (2)
Nucleosomes consists of DNA wrapped around 8 histone proteins
Held together by another histone protein (H1 linker)

7.1.3 State that nucleosomes help to supercoil chromosomes(1)
Nucleosomes help to super-coil chromosomes and help to regulate transcription
Super coil to factor x 15,000
Super coiled areas cannot be transcribed
Allows control over which genes are expressed

7.1.4 Distinguish between unique and highly repetitive sequences in nuclear DNA (2)
Unique/single-copy genes:
Gene coding region
Approx 1.5% of our DNA codes for a particular polypeptide
3% codes for on/off switches
Highly repetitive sequences:
5 45% of the genome
Once called junk DNA
Non-coding/ not translated
Consists of sequences from 5 300 base pairs long
Used in genetic fingerprinting because they accumulate mutations fast

7.1.5 State that eukaryotic genes can contain exons and introns (1)
Eukaryotic genes can contain exons and introns


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7.2 DNA replication
7.2.1 State that DNA replication occurs in a 5 3 direction (1)
DNA replication occurs in a 5 3 direction

7.2.2 Explain the process of DNA replication in prokaryotes (3)
Process of DNA replication:
DNA replication occurs during S-phase of interphase

1. Enzyme helicase unzips and unwinds the DNA double helix by breaking apart the hydrogen
bonds between bases into two parent strands
2. Enzyme DNA Polymerase III collects free nucleotides from within the nucleus and creates
two complementary strands
3. Initially they are nucleoside triphosphates (base, sugar with 3 phosphate groups). However,
2 of these phosphate groups break off to provide energy for the synthesis reaction between
base of parent strand and new strand
4. Because DNA replication occurs in a 5 3 direction, will form a leading strand and lagging
strand
Leading strand replicates continuously (same direction as replication fork)
Lagging strand replicates in a leap frog motion (away from replication fork)
In the case of the lagging strand, RNA primase acts as primers and leaves markers
for DNA polymerase III
DNA polymerase III replicates small segments of DNA at a time (known as Okazaki
fragments)
5. DNA polymerase I replaces RNA primers with DNA
6. DNA ligase then joins the Okazaki fragments into one continuous strand

7.2.3 State that DNA replication is initiated at many points in eukaryotic chromosomes (1)
DNA replication is initiated at many points in eukaryotic chromosomes (replication bubbles)

7.3 Transcription
7.3.1 State that transcription is carried out in a 5 3 direction (1)
Transcription is carried out in a 5 3 direction
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7.3.2 Distinguish between the sense strand and anti-sense strands of DNA (2)
The sense strand is the coding strand with the same base sequence as the transcribed mRNA,
except thymine is replaced by uracil.
The anti-sense strand is the template strand, or non-coding strand which is used for
transcription (making the RNA)

7.3.3 Explain the process of transcription in prokaryotes (3)
Process of transcription in prokaryotes:
Occurs during S phase of interphase in preparation for mitosis/cell division
Occurs in 4 stages:

1. Initiation:
The promoter region allows binding of RNA polymerase, which can then find start
of anti-sense strand, start for transcription and know the direction of transcription
DNA helicase unwinds and unzips DNA, exposing the bases of the anti-sense strand
progressively (in 3 5 direction)
RNA nucleotides form complementary base pairs with anti-sense polynucleotide
strand
Complementary base pairing remain in almost the same order except thymine is
replaced by uracil

2. Elongation
RNA polymerase forms covalent bonds between nucleotides
Energy is released through oxidation of nucleoside triphosphates to synthesize
reaction
Bonds are formed by joining the 5 of a free nucleotide to the 3 of a nucleotide
already part of the mRNA chain
RNA polymerase works along nucleotides until pentose-phosphate backbone is
complete

3. Termination
RNA polymerase reaches the terminator site and the enzyme stops
mRNA is complete

7.3.4 State that eukaryotic RNA needs the removal of introns to form nature mRNA (1)
Eukaryotic RNA needs the removal of introns to form mature mRNA
Before transcription, mRNA processing occurs:
1. Introns are removed (by spliceosomes)
2. Extrons are spliced together
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3. The mRNA is capped at the ends protects mRNA from being broken down


7.4 - Translation
7.4.1 Explain that each tRNA molecule is recognised by a tRNA-activating enzyme (3)
tRNA molecules have a general clover-leaf structure with three loops
Each tRNA molecule has a different structure and contains double stranded sections (due to
H-bond between base pairs) and loops
Each tRNA molecule is recognized by a tRNA-activating enzyme (aminoacyl-tRNA synthetase)
that binds specific amino acid to the tRNA due to different chemical properties and 3D
structures
Binding process uses ATP for energy
Amino acid binding site at 3 end, with CCA nucleotide sequence

7.4.2 Outline the structure of ribosomes, including protein and RNA composition, large and small
subunits, three tRNA binding sites and mRNA binding sites (2)
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Ribosomes are made of protein and rRNA (ribosomal RNA)
Consists of small subunit and large subunit
Small subunit: has the mRNA binding site
Large subunit: has 3 sites A, P and E

o A site holds the tRNA carrying next amino acid
o P bonds form; holds tRNA attached to growing polypeptide strand
o E tRNA is discharged

7.4.3 State that translation consists of initiation, elongation, translocation and termination (1)
Translation consists of initiation, elongation, translocation and termination.
Initiation:
Ribosome meets mRNA at MET codon (start codon: AUG)
First tRNA is brought in
Elongation:
Peptide bond is formed between amino acids, forming a polypeptide chain
tRNA binds to codon which corresponds with its anticodon amino acids are added
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Translocation:
Ribosome releases used tRNA and moves along to the next codon
More tRNA and amino acids are brought in, lengthening the chain
Termination:
Ribosome reaches stop codon
Polypeptide is released

7.4.4 State that translation occurs in a 5 3 direction (1)
Translation occurs in a 5 3 direction

7.4.5 Draw and label a diagram showing the structure of a peptide bond b/w two amino acids (1)


7.4.6 Explain the process of translation, including ribosomes, polysomes, start/stop codons (3)
The process of translation occurs in the following steps:
1. Translation occurs in the cytoplasm ribosomes
2. Ribosomes consists of 2 parts small and large subunits
3. Small subunit binds to the mRNA, whilst large subunit has 3 sites A, P and E
4. tRNA carrying anti-codon UAC for methionine (complementary to start codon AUG) and
occupies the P site
5. A site is free for other complementary tRNA to bind
6. tRNA enters the A site carrying the amino acid according to its anti-codon base sequence,
which is complementary to the codon on the mRNA section it is attached to
7. The amino acids are joined together through peptide bonds (condensation reaction)
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8. Methionine breaks away energy released allows MET to bond with amino acid on the tRNA
in the A site
9. The used tRNA leaves through the E site
10. More tRNA is brought in and the chain lengthened
11. This process continues until the ribosome reaches a STOP codon
12. At the stop codon, the polypeptide is released
13. The one strand of mRNA can be translated by multiple ribosomes at the same time then
they are known as polysomes

7.4.7 State that free ribosomes synthesise proteins for use primary within the cell(1)
Free ribosomes synthesize proteins for use primarily within the cell

Bound ribosomes (attached to the wall of the rough ER) synthesize proteins primarily for
secretion via vesicles or for lysosomes.