Transcript 7.2.7 Describe the promoter as an example of non-coding

AHL Transcription & Translation (7.2-7.3)
IB Diploma Biology
An SEM micrograph of Ribosomes
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.
7.2.7 Describe the promoter as an example of non-coding DNA with a
function.
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.
Adjacent gene is transcribed while
promoter region is not.
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…
7.2.1 Gene expression is regulated by proteins that bind to specific base
sequences in DNA.
• 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.U5 Gene expression is regulated by proteins that bind to specific base sequences in DNA.
One well known example of the regulation of gene expression by proteins is the
metabolism of lactose in E. Coli bacterium. The diagram below illustrates this example.
RNA Polymerase
The repressor protein is bound
to the operator preventing RNA
Polymerase from transcription
of the genes
DNA Strand
Operator is a region of DNA
that can regulate transcription,
typically inhibiting
transcription, such as this
silencer sequence.
The promoter is a DNA
sequence is located near a
gene. It acts as the binding
site for RNA polymerase.
Genes involved in
the metabolism
(breakdown) of
lactose
The consequence of the inhibition of the lactose
metabolism is that the concentration of
undigested lactose now increases in E. Coli …
Edited from: http://commons.wikimedia.org/wiki/File:Lac_Operon.svg
7.2.U5 Gene expression is regulated by proteins that bind to specific base sequences in DNA.
One well known example of the regulation of gene expression by proteins is the
metabolism of lactose in E. Coli bacterium. The diagram below illustrates this example.
Lactose binds to the repressor protein
inhibiting it: the repressor can no
longer bind to the operator.
RNA polymerase binds with the
promoter, and express the genes (by
transcribing them), which in turn
synthesizes lactase
Lactose molecules build up
inside the E. Coli
With the synthesis of lactase the lactose
is broken down, as it’s concentration
decreases the inhibition of the repressor
molecules will decrease ‘silencing’ the
gene again.
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)
7.2.U5 Gene expression is regulated by proteins that bind to specific base sequences in DNA.
Summary of common types of regulating proteins and associated sequences
found in eukaryotes.
DNA
Sequence
Binding protein
Function
Enhancers
Activator
Activator proteins bind to enhancer sequences
of DNA to greatly increase the rate of
transcription of a gene.
Silencers
Repressor
Repressor proteins bind to non-coding regions
of DNA to either block or reduce the
transcription of a gene.
Promoter
RNA
Polymerase
A region of DNA located close to a specific
gene. Once bound to the sequence RNA
polymerase transcribes the gene.
7.2.2 The environment of a cell and of an organism has an impact on gene
expression.
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.
In embryonic development, chemicals called
morphogens activate gene expression in cells
depending on where they are in the embryo
to allow for tissue differentiation.
Morphogenes regulate the production of
transcription factors in a cell. This results in
the activation and inhibition of different
genes in different cells. This in turn controls
how long your fingers should be, where your
nose is on your face, and other specifics
about body structure.
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)
7.2.U6 The environment of a cell and of an organism has an impact on gene expression.
The environment of an organism impacts
gene expression. For example human hair
and skin colour are impacted by the exposure
to sunlight and high temperatures.
Similarly pigments in the fur of Himalayan
rabbits (Oryctolagus cuniculus) are
regulated by temperature.
Gene C controls fur pigmentation in Himalayan rabbits. The
gene is active when environmental temperatures are between
15 and 25°C. At higher temperatures the gene is inactive.
In low temperatures Gene C becomes active in the
rabbit's colder extremities (ears, nose, and feet)
and produces a black pigment.
In the warm weather no
pigment is produced
and the fur is white
http://upload.wikimedia.org/wikipedia/commons/0/06/Kr%C3%B3liki_kalifornijskie_666.jpg
http://www.alpinecommunitynetwork.com/wp-content/uploads/himalayan-bunny-5-19-11-1_opt4.jpg
7.2.3 Nucleosomes help to regulate transcription in eukaryotes.
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.U2 Nucleosomes help to regulate transcription in eukaryotes.
Methylation is the addition of
methyl groups to DNA
Methylation of DNA inhibits transcription
*Chromatin is a complex of DNA, protein and
RNA. Tightly packed chromatin which cannot be
transcribed is referred to as heterochromatin.
Processes that inhibit transcription bind
the DNA more tightly to the histone
making it less accessible to transcription
factors (forming heterochromatin).
Edited from: http://www.nature.com/neuro/journal/v13/n4/images/nn0410-405-F1.jpg
7.2.U2 Nucleosomes help to regulate transcription in eukaryotes.
Acetylation is the addition of Acetyl
groups to histones
Acetylation promotes transcription
n.b. Methylation of histones can also
occur, this process can both promote
and inhibit transcription.
Processes that promote transcription
bind the DNA more loosely to the
histone making it more accessible to
transcription factors (forming
euchromatin*).
*Chromatin is a complex of DNA, protein and
RNA. Loosely packed chromatin which can be
transcribed is referred to as euchromatin.
Edited from: http://www.nature.com/neuro/journal/v13/n4/images/nn0410-405-F1.jpg
7.2.3 Nucleosomes help to regulate transcription in eukaryotes.
7.2.U2 Nucleosomes help to regulate transcription in eukaryotes.
Changes in the environment affect the cell metabolism, this in turn can directly or indirectly
affect processes such as Acetylation & Methylation.
Methylation and acetylation mark the DNA to affect
transcription. These these markers are known as
epigenetic tags*.
For a new organism to
grow it needs unmarked
DNA that can develop into
lots of different specialised
cell types.
Reprogramming scours the genome and erases the epigenetic
tags to return the cells to a genetic "blank slate”.
*The branch of genetics concerned with
hertible changes not caused by DNA is
called Epigenetics.
For a small number of genes, epigenetic tags make it through this
process unchanged hence get passed from parent to offspring.
http://learn.genetics.utah.edu/content/epigenetics/inheritance/images/Reprogramming.jpg
7.2.8 Analyze changes in DNA methylation patterns.
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)
7.2.4 Transcription occurs in a 5’ to 3’ direction.
5’
3’
7.2.5 Eukaryotic cells modify mRNA after transcription.
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
http://bcs.whfreeman.com/thelifewire/co
ntent/chp14/1401s.swf
7.2.5 Eukaryotic cells modify mRNA after transcription.
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)
7.2.6 Splicing of mRNA increases the number of different proteins an
organism can produce.
• 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.
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
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
7.3.11 tRNA-activating enzymes illustrate enzyme-substrate specificity and
the role of phosphorylation.
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
http://highered.mheducation.com/sites/9834092339/stud
ent_view0/chapter15/aminoacyl_trna_synthetase.html
7.3.1 Initiation of translation involves assembly of the components that carry
out the process
P-site of ribosome
A-site of ribosome
7.3.2 Synthesis of the polypeptide involves a repeated cycle of events.
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
7.3.3 Disassembly of the components follows termination of translation
7.3.3 Disassembly of the components follows termination of translation
http://www.stolaf.edu/people/giannini/flashanimat/molgen
etics/translation.swf
http://highered.mheducation.com/sites/0072507470/st
udent_view0/chapter3/animation__how_translation_w
orks.html
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.
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.
7.3.13 Identify polysomes in an electron micrograph.
• Polysome: Many ribosomes simultaneously translating the same
mRNA (allows for faster protein synthesis)
• Polysomes appear as beads on a
string in electron micrographs
• “Beads” represent multiple
ribosomes attached to a single
mRNA molecule
• Poly = many, some = ribosome
7.3.6 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.
http://www.stolaf.edu/people/giannini/flashan
imat/proteins/protein%20structure.swf
Bibliography / Acknowledgments
Darren Aherne
Chris Paine