Slides covering Additional Higher Level (AHL) material from Topic 7.2 and 7.3 of the updated IB Biology syllabus for 2016 exams

1. AHL Transcription & Translation (7.2-7.3)
IB Diploma Biology
An SEM micrograph of Ribosomes

2. 7.2.7 Describe the promoter as an example of non-coding DNA with a
function.
• Only some DNA sequences code for synthesis of polypeptides
(single-copy genes)
• Non-coding regions (highly-repetitive sequences) have other
functions:
 tRNA production
 rRNA production (ribosomal RNA)
 Control gene expression
Enhancers: regulatory sequences on DNA which
increase the rate of transcription when proteins
bind to them.
Silencers: sequences on DNA which decrease the
rate of transcription when proteins bind to them.

3. The Promoter is located near a
gene’s location. It is the binding
site of RNA polymerase--the
enzyme that constructs mRNA
from the DNA template during
Transcription.
7.2.7 Describe the promoter as an example of non-coding DNA with a
function.

4. 7.2.7 Describe the promoter as an example of non-coding DNA with a
function.
A more complex view of Transcription initiation, including the role
of enhancer regions of the DNA sequence…

5. • Some proteins are always needed by an organism and so they are
constantly being produced…
• Other proteins are only needed at certain times or in limited
amounts so their production must be controlled…
• Gene expression is regulated by environmental factors
• Proteins bind to Enhancer sequences to increase transcription
of genes for protein synthesis
• Proteins bind to Silencer sequences to decrease or inhibit
transcription of genes for protein synthesis
7.2.1 Gene expression is regulated by proteins that bind to specific base
sequences in DNA.

6. 7.2.1 Gene expression is regulated by proteins that bind to specific base
sequences in DNA.
Example: In E. coli the genes for proteins that digest lactose are silenced
unless there is lactose in the cell (lactose binds to the silencer proteins,
removing them from the genes so they can be transcribed)

7. Epigenetics: the study of changes in
organisms caused by modification of
gene expression rather than alteration
of the genetic code itself…
Scientists and philosophers have long
debated whether ‘nature’ (genes) or
‘nurture’ (environment) determines
the traits and fates of organisms
Epigenetics has shown that both play
a substantial role as gene expression
is clearly impacted by a cell’s
environment (ex. human skin cells
producing more melanin in high-sun
environments…
7.2.2 The environment of a cell and of an organism has an impact on gene
expression.

8. 7.2.2 The environment of a cell and of an organism has an impact on gene
expression.
In embryonic development, chemicals
called morphogens activate gene
expression in cells depending on where
they are in the embryo to allow for
tissue differentiation
Siamese cats have been selectively-
bred for a mutated pigment protein
that is only expressed at temperatures
below body temperature (thus, these
cats only show coloring in their
extremities – ears, paws, etc. – where
temperatures are lower)

9. Eukaryote DNA is associated with histone proteins which
wind the DNA to form units called nucleosomes
The histone protein tails can be modified:
• Acetyl group: neutralizes the positive charge on histones,
making DNA less tightly coiled–> increases transcription
• Methyl group: maintains positive charge on histones,
making DNA tightly coiled –> decreases transcription
http://learn.genetics.utah.edu/content/epig
enetics/control/
7.2.3 Nucleosomes help to regulate transcription in eukaryotes.

10. 7.2.3 Nucleosomes help to regulate transcription in eukaryotes.

11. Direct methylation of DNA (not to histone
tails) is thought to affect gene expression.
• Increased methylation of DNA decreases
gene expression
• DNA methylation is variable during
our lifetime
• Amount of methylation depends on
environmental factors, like diet
• Evidence for heritability of
methylated DNA
• EX: Diet of pregnant mice has been shown to
influence weight and fur color of offspring (left)
7.2.8 Analyze changes in DNA methylation patterns.

12. 7.2.4 Transcription occurs in a 5’ to 3’ direction.
5’ 3’

13. http://bcs.whfreeman.com/thelifewire/co
ntent/chp14/1401s.swf
Introns are Interruptions within
the coding sequences of a gene
transcript (mRNA)
Exons are the Expressed sections
of the gene transcript (mRNA)
that are translated into
polypeptides
7.2.5 Eukaryotic cells modify mRNA after transcription.

14. In addition to splicing out the Introns from the pre-mRNA, a 5’
cap is added to the mRNA transcript and a Poly-A tail is
added to the 3’ end to protect against degradation of the
coding sections of the mRNA (similar to telomeres in DNA)
7.2.5 Eukaryotic cells modify mRNA after transcription.

15. • The Proteome (set of proteins) of an organism is actually much
larger than its Genome (set of genes)
• The main way there can be more proteins than there are genes is
due to Alternative Splicing:
• Proteins are often translated from mRNA with multiple exons.
• The exons can be spliced together differently, result in in a different sequence of
amino acids.
• Consequently, a number of different protein structures and functions are possible
from the same mRNA
• 1 fruit fly gene can produce 38,000 different mRNAs / proteins based on the
different ways it’s exons can be spliced together!
7.2.6 Splicing of mRNA increases the number of different proteins an
organism can produce.

16. 7.2.6 Splicing of mRNA increases the number of different proteins an
organism can produce.

17. 7.3.12 Use molecular visualization software to analyze the structure of
eukaryotic ribosomes and a tRNA molecule.
Ribosome Structure:
• Made up of proteins and ribosomal RNA (rRNA)
• Large subunit (50S) & small subunit (30S) – make up 80S ribosome
• 3 binding sites for tRNA (A site, P site, E site)
• tRNA enters A site, shifts to P site, and exits E site
• 2 tRNAs can bind to the surface of the ribosome at a time, 1 mRNA
can bind to surface of small subunit

18. 7.3.12 Use molecular visualization software to analyze the structure of
eukaryotic ribosomes and a tRNA molecule.
tRNA Structure:
• Double stranded sections by
complementary base pairing
• Anticodon of 3 bases in a 7-base loop
• 2 other loops
• 3’ end has amino acid binding site
with CCA sequence of unpaired bases

19. 7.3.11 tRNA-activating enzymes illustrate enzyme-substrate specificity and
the role of phosphorylation.

20. http://highered.mheducation.com/sites/9834092339/stud
ent_view0/chapter15/aminoacyl_trna_synthetase.html
7.3.11 tRNA-activating enzymes illustrate enzyme-substrate specificity and
the role of phosphorylation.
http://www.phschool.com/science/biology
_place/biocoach/translation/addaa.html

21. 7.3.1 Initiation of translation involves assembly of the components that carry
out the process
P-site of ribosome
A-site of ribosome

22. Elongation:
A series of repeated steps…
• Ribosome moves 3 bases (one codon) along the mRNA (5’ -> 3’)
• tRNA at P-site moves to E-site, allowing it to disengage
• tRNA complementary to the codon at A-site enters
• Peptide bond forms between AA’s in A and P sites
• Process continues many times
7.3.2 Synthesis of the polypeptide involves a repeated cycle of events.

23. 7.3.3 Disassembly of the components follows termination of translation

24. http://highered.mheducation.com/sites/0072507470/st
udent_view0/chapter3/animation__how_translation_w
orks.html
http://www.stolaf.edu/people/giannini/flashanimat/molgen
etics/translation.swf
7.3.3 Disassembly of the components follows termination of translation

25. Location of protein synthesis: cell
functions & protein synthesis are
compartmentalized (by organelles)
• Proteins that will be used by the
cell in cytoplasm, mitochondria,
and chloroplasts are synthesized
on free ribosomes in the
cytoplasm
• Proteins that will be secreted or
used by lysosomes are
synthesized on bound ribosomes
found on the RER
7.3.4 Free ribosomes synthesize proteins for use primarily within the cell /
7.3.5 Bound ribosomes synthesize proteins primarily for secretion or for use
in lysosomes.

26. 7.3.4 Free ribosomes synthesize proteins for use primarily within the cell /
7.3.5 Bound ribosomes synthesize proteins primarily for secretion or for use
in lysosomes.

27. • Polysomes appear as beads on a
string in electron micrographs
• “Beads” represent multiple
ribosomes attached to a single
mRNA molecule
• Poly = many, some = ribosome
7.3.13 Identify polysomes in an electron micrograph.
• Polysome: Many ribosomes simultaneously translating the same
mRNA (allows for faster protein synthesis)

28. 7.3.6 Translation can occur immediately after transcription in prokaryotes
due to the absence of a nuclear membrane.
In prokaryotes, since there is no
nucleus, transcription and translation
can be directly coupled (see below).
Ribosomes attach to the mRNA as it is
being synthesized from the DNA
template.

29. http://www.stolaf.edu/people/giannini/flashan
imat/proteins/protein%20structure.swf

30. Bibliography / Acknowledgments
Darren Aherne
Chris Paine