1. DNA Protein Synthesis Review: Topic 7.1 – 7.4

2. 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines
The carbon atoms in deoxyribose are numbered, with the nitrogenous bases attach to C1 and the phosphate group is attached to C5
Nucleotides are joined by a covalent
phosphodiester bond between the
C5 phosphate group and the C3 hydroxyl
group
Hence one nucleotide
strand runs 5' - 3‘ OH O 3
PO4
base
CH2 P C –O 1 2 4 5 OH
CH2 O 4 5 3 2 1
PO4
N base
ribose
nucleotide

3. 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines
Adenine (A) and thymine (T) share 2 hydrogen bonds
Guanine (G) and cytosine (C) share 3 hydrogen bonds
In order for the bases to associate (i.e. face each other), one strand must run antiparallel to the other (this antiparallel strand runs 3' - 5') 
Double stranded DNA forms a double helix,
with 10 nucleotides per turn and the structure
containing both
major and minor
grooves

4. 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines

5. 7.1.2  Outline the structure of nucleosomes
The DNA double helix contains major and minor grooves
on its outer diameter, which expose chemical groups that
can form hydrogen bonds
The DNA of eukaryotes associates with proteins called
histones
DNA is wound around an octamer of histones (146 bases
and 1.65 turns of the helix per octamer)
The octamer and DNA combination is secured to a H1
histone, forming a nucleosome 

6. 7.1.2  Outline the structure of nucleosomes

7. 7.1.3  State that nucleosomes help to supercoil DNA and help
to regulate transcription
Nucleosomes serve two main functions:
They protect DNA from damage
They allow long lengths of DNA to be packaged (supercoiled)
for mobility during mitosis / meiosis
When supercoiled, DNA is not accessible for transcription
Cells will have some segments of DNA permanently
supercoiled (heterochromatin) and these segments will differ
between different cell types

8. 7.1.4  Distinguish between unique or single copy genes and
highly repetitive sequences in nuclear DNA

9. 7.1.5 State that eukaryotic genes contain introns and exons
Intron:  A non-coding sequence of DNA within a gene
(intervening sequence) that is cut out by enzymes
when RNA is made into mature mRNA
Exon: The part of the gene which codes for a protein
(expressing sequence)
Eukaryotic DNA contains introns but prokaryotic DNA
does not
eukaryotic DNA
exon = coding (expressed) sequence
intron = noncoding (in between) sequence

10. 7.2.1  State that DNA replication occurs in a 5' - 3' direction
DNA replication is semi-conservative, meaning that a new
strand is synthesized from an original template strand
DNA replication occurs in a 5' - 3' direction, in that new
nucleotides are added to the C3 hydroxyl group such that
the strand grows from the 3' end
This means that the DNA polymerase enzyme responsible
for adding new nucleotides moves along the original
template strand in a 3' - 5' direction

11. DNA replication is semi-conservative and occurs during the
7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates
DNA replication is semi-conservative and occurs during the
S phase of interphase
Helicase unwinds and separates the double stranded DNA
by breaking the hydrogen bonds between base pairs
RNA primase synthesizes a short RNA primer on each
template strand to provide an attachment and initiation point
for DNA polymerase III

12. DNA polymerase III adds deoxynucleoside triphosphates
7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates
DNA polymerase III adds deoxynucleoside triphosphates 
(dNTPs) to the 3' end of the polynucleotide chain, synthesizing
in a 5' - 3' direction
The dNTPs pair up opposite their complementary base partner
(A-T, G-C)
As the dNTPs join with the DNA chain, two phosphates are
broken off, releasing the energy needed to form a
phosphodiester bond
energy
energy
ATP
GTP
TTP
CTP

13. Synthesis is continuous on the strand moving towards the
7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates
Synthesis is continuous on the strand moving towards the
replication fork (leading strand) 
Synthesis is discontinuous on the strand moving away from the
replication fork (lagging strand) leading to the formation
of Okazaki fragments
DNA polymerase I removes the RNA primers and replaces them
with DNA
DNA ligase joins the Okazaki fragments together to create a
continuous strand

14. 7.2.3  State that DNA replication is initiated at many points in
eukaryotic chromosomes
Because eukaryotic genomes are (typically) much larger than
prokaryotic genomes, DNA replication is initiated at many
points simultaneously in order to limit the time required for
DNA replication to occur
The specific sites at which DNA unwinding and initiation of
replication occurs are called origins of replication and form
replication bubbles
As replication bubbles expand in both directions, they
eventually fuse together, and generate two separate semi-
conservative double strands of DNA

15. 7.3.1  State that transcription is carried out in a 5' - 3'
direction
Transcription is carried out in a 5' - 3' direction (of the new
RNA strand)

16. 7.3.2  Distinguish between the sense and antisense strands
of DNA
DNA consists of two polynucleotide strands, only one of which
is transcribed into RNA
The antisense strand is transcribed into RNA
- sequence will be complementary to the RNA sequence
and will be the "DNA version" of the tRNA anticodon
sequence 
The sense strand is not transcribed into RNA
- Its sequence will be the "DNA version" of the RNA
sequence (identical except for T instead of U)

17. 7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator
A gene is a sequence of DNA which is transcribed into RNA
and contain three main parts:
Promoter:  Responsible for the initiation of transcription (in
prokaryotes, a number of genes may be regulated by a single
promoter - this is an operon)
Coding Sequence:  The sequence of DNA that is actually
transcribed (may contain introns in eukaryotes)
Terminator:  Sequence that serves to terminate transcription
(mechanism of termination differs between prokaryotes and
eukaryotes)

18. 7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator
Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence and involves a number of steps:
RNA polymerase binds to the promoter and causes the
unwinding and separation of the DNA strands
Nucleoside triphosphates (NTPs) bind to their
complementary bases on the antisense strand (uracil pairs
with adenine, cytosine pairs with guanine)
RNA polymerase covalently binds the NTPs together in a
reaction that involves the release of two phosphates to gain
the required energy

19. 7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator
RNA polymerase synthesizes an RNA strand in a 5' - 3'
direction until it reaches the terminator
At the terminator, RNA polymerase and the newly formed
RNA strand both detach from the antisense template, and the
DNA rewinds
Many RNA polymerase enzymes can transcribe a DNA
sequence sequentially, producing a large number of
transcripts
Post-transcriptional modification is necessary in eukaryotes

20. Euakaryotic genes may contain non-coding sequences
7.3.4  State that eukaryotic RNA needs the removal of introns to form mature mRNA
Euakaryotic genes may contain non-coding sequences
called introns that need to be removed before mature
mRNA is formed
The process by which introns are removed is called
splicing
The removal of exons (alternative splicing) can generate
different mRNA transcripts (and different polypeptides)
from a single gene
eukaryotic DNA
exon = coding (expressed) sequence
intron = noncoding (inbetween) sequence
primary mRNA
transcript
mature mRNA
pre-mRNA
spliced mRNA
~10,000 bases
~1,000 bases

21. 7.4.1  Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA using ATP for energy
Each different tRNA molecule has a unique shape and
chemical composition that is recognized by a specific tRNA-
activating enzyme
The enzyme (aminoacyl-tRNA synthetase)
first binds the amino acid to a molecule
of ATP (to form an  amino acid-AMP
complex linked by a high energy bond)

22. 7.4.1  Explain that each tRNA molecule is recognised by a tRNA-activating enzyme that binds a specific amino acid to the tRNA using ATP for energy
The amino acid is then transferred to
the 3'-end of the appropriate tRNA,
attaching to a terminal CCA sequence
on the acceptor stem and releasing the
AMP molecule
The tRNA molecule with an amino acid
attached is thus said to be 'charged' and
is now capable of participating in
translation
The energy in the bond linking the
tRNA molecule to the amino acid
will be used in translation to form a
peptide bond between adjacent amino acids

23. Ribosomes are made of protein (for stability) and ribosomal
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
Ribosomes are made of protein (for stability) and ribosomal
RNA (rRNA - for catalytic activity)
They consist of two subunits:
- The small subunit contains an mRNA binding site
The large subunit contains three tRNA binding sites - an
aminacyl (A) site, a peptidyl (P) site and an exit (E) site
Met 5' 3' U A C G P E

24. 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
Ribosomes can be either found freely in the cytosol or bound
to the rough ER (in eukaryotes)
Ribosomes differ in size in eukaryotes and prokaryotes
(eukaryotes = 80S ; prokaryotes = 70S) E

25. 7.4.3  State that translation consists of initiation, elongation, translocation and termination
Translation occurs in four main steps:
Initiation:  Involves the assembly of an active ribosomal
complex
Elongation:  New amino acids are brought to the ribosome
according to the codon sequence
Translocation:  Amino acids are translocated to a growing
polypeptide chain
Termination:  At certain "stop" codons, translation is ended
and the polypeptide is released E

26. 7.4.4 State that translation occurs in a 5' - 3' direction
The start codon (AUG) is located at the 5' end of the mRNA
sequence and the ribosome moves along it in the 3' direction
Hence translation occurs in a 5' - 3' direction
Leu
tRNA
Met P E A
mRNA 5' 3' U C G
Val
Ser
Ala
Trp
release
factor

27. 7.4.5  Draw and label a diagram showing the structure of a peptide bond between two amino acids

28. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons
Pre-Initiation:
Specific tRNA-activating enzymes catalyze the attachment
of amino acids to tRNA molecules, using ATP for energy
Initiation: 
The small ribosomal subunit binds to the 5' end of mRNA
and moves along it until it reaches the start codon (AUG)
Next, the appropriate tRNA molecule binds to the codon
via its anticodon (according to complementary base pairing)
Finally, the large ribosomal subunit aligns
itself to the tRNA molecule at its P-site
and forms a complex with the small
ribosomal subunit

29. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons
Elongation:
A second tRNA molecule pairs with the next codon in
the ribosomal A-site
The amino acid in the P-site is covalently attached via a
peptide bond to the amino acid in the A-site

30. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons
Translocation:
The ribosome moves along one codon position, the
deacylated tRNA moves into the E-site and is released,
while the tRNA bearing the dipeptide moves into the P- site
Another tRNA molecules attaches to the next codon in the
newly emptied A-site and the process is repeated
The ribosome moves along the mRNA sequence in a 5' - 3'
direction, synthesizing a polypeptide chain
Multiple ribosomes can translate a single mRNA sequence
simultaneously (forming polysomes)

31. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons
Termination: 
Elongation and translocation continue until the ribosome
reaches a stop codon
These codons do not code for any amino acids and instead
signal for translation to stop
The polypeptide is released and the ribosome disassembles
back into subunits
The polypeptide may undergo post-translational modification
prior to becoming a functional protein

32. 7.4.7  State that free ribosomes synthesis proteins for use primarily within the cell, and that bound ribosomes synthesis proteins primarily for secretion or for lysosomes
Ribosomes floating freely in the cytosol produce proteins for
use within the cell
Ribosomes attached to the rough ER are primarily involved in
producing proteins to be exported from the cell or used in the
lysosome
These proteins contain a signal recognition peptide on their
nascent polypeptide chains which direct the associated
ribosome to the rough ER

33. 7.4.7  State that free ribosomes synthesis proteins for use primarily within the cell, and that bound ribosomes synthesis proteins primarily for secretion or for lysosomes
(How DNA is packaged)
(transcription)
(translation)
(DNA replication)
(replication, transcription, translation)