Dna Proteins and Binding to ligands Think What proteins are associated with DNA How are proteins involved in transcription How is protein production controlled Why is it important that protein production is controlled ID: 909706
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Slide1
Advanced Higher Cells and Proteins
Dna
, Proteins and Binding to ligands
Slide2Think
What proteins are associated with DNA?
How are proteins involved in transcription?
How is protein production controlled?
Why is it important that protein production is controlled?
Why is protein structure important in relation to its function?
Slide3DNA and proteins
This lesson will cover
DNA and its associated proteins
Other proteins involved with transcription
Slide4DNA and protein association
Slide5DNA and protein association
DNA binds to a number of proteins.
Positively charged histone proteins bind to the
negatively charged sugar-phosphate backbone of
DNA in eukaryotes.
DNA is wrapped around histones to form nucleosomes
packing the DNA in chromosomes.
Slide6DNA and protein association
Animation
Slide7Histone proteins and nucleosome
Slide8Other DNA proteins and ligand binding
Other proteins have binding sites that are specific to
particular sequences of double stranded DNA.
When this happens they can stimulate or inhibit the
initiation of transcription.
Animation
Slide9Dna
and protein complex in transcription
Slide10Transcription Factors
Transcription factors (TFs) are molecules involved in
regulating gene expression.
They
are usually proteins,
(they
can
be short
, non-coding
RNA).
TFs
are also usually found working in groups or
complexes
, forming
multiple
interactions
that allow for varying degrees
of control
over rates of
transcription.
Slide11Transcription Factors
In people (and other eukaryotes), genes are usually in a
default "
off
" state, so TFs serve mainly to turn gene expression "
on
".
TFs work by recognizing certain nucleotide sequences (
motifs) before
or after the gene on the
chromosome.
The TFs bind, attract other TFs and create a complex
that eventually
facilitates
binding
by RNA polymerase, thus
beginning the
process of transcription.
Slide12Binding changes the conformation of a protein
Proteins including enzymes are three-dimensional and have a specific shape or conformation.
As a ligand binds to a protein binding site, or a substrate binds to an enzyme’s active site, the conformation of the protein changes.
This change in conformation causes a functional change in the protein and may activate or deactivate it.
Slide13Binding to ligands
A ligand is a substance that can bind to a protein.
R groups not involved in protein folding can allow binding to these other molecules.
Binding sites will have complementary shape and chemistry to the ligand.
The ligand can either be a substrate or a molecule that affects the activity of the protein.
Slide14All chemical reactions require energy to enable them, this is the
activation energy
.
Enzymes lower the activation energy.
2 types of reaction are:
Anabolic (synthesis) a dehydration synthesis reaction.
Catabolic (degradation) a hydrolysis reaction
.
Enzymes
Slide15Anabolic Reactions
Uses energy to SYNTHESISE large molecules from smaller ones e.g.
Amino Acids Proteins
Also known as endothermic reactions
ENDOTHERMIC REACTION
Slide16Catabolic Reactions
These release energy through the BREAKDOWN of large molecules into smaller units e.g.
Cellular Respiration:
ATP ADP + Pi
Also known as exothermic reactions
EXOTHERMIC REACTION
Slide17Enzyme types
Proteases
- break down proteins into amino acids by breaking peptide bonds (hydrolysis).
Nucleases
- break down nucleic acids into nucleotides (hydrolysis).
ATPases
- hydrolysis of ATP
.
Kinases
- add phosphate groups to molecule
.
Phosphatases
– remove phosphate groups
Slide18Control of Enzyme activity
Control of enzyme activity occurs in these ways
number of enzyme molecules present
compartmentalisation
change of enzyme shape by
competitive inhibitors, non-competitive inhibitors,
enzyme modulators, covalent modification
end product inhibition
Slide19How do enzymes work?
Slide20Induced fit and enzymes
Enzymes are not necessarily a perfect sit to substrate
The enzyme changes shape in response to close association with the substrate.
This the Induced fit theory
Slide21A molecule close to shape of substrate
competes
directly
for active site so reducing the concentration of available enzyme.
This can be reversed by increasing the concentration of the correct substrate unless the binding of competitor is irreversible.
Competitive inhibition
Slide22Succinate dehydrogenase
catalyses
the oxidation of succinate to fumarate (respiration)
Malonate is the competitive inhibitor
Malonate example
Slide23Slide24An inhibitor binds to the enzyme molecule at a
different area
and
changes the shape
of the enzyme including the active site.
This may be a permanent alteration or may not.
Non-competitive inhibition
Slide25Slide26Inhibition can either be reversible or non-reversible
Some inhibitors bind irreversibly with the enzyme molecules.
The enzymatic reactions will stop sooner or later and are not affected by an increase in substrate concentration.
Irreversible inhibitors include heavy metal ions such as silver, mercury and lead ions.
Slide27Some enzymes
change their shape
in response to a
regulating molecule
.
These are called allosteric enzymes
Positive modulators (activators)
stabilise enzyme in the active form.
Negative modulators (inhibitors)
stabilise enzyme in the inactive form.
Enzyme modulators
Slide28Allosteric Enzymes
Slide29Involves the addition, modification or removal of a variety of chemical groups to or from an enzyme
(
often phosphate.)
These result in a change in the shape of the enzyme and so its activity.
These include phosphorylation by kinases and
dephosphorylation
by phosphatases.
Conversion of inactive forms to active forms e.g. trypsinogen and trypsin
Covalent modifications
Slide30An example of activation is trypsinogen to trypsin
trypsinogen activated by
enterokinase
in duodenum
Slide31Trypsin is synthesised in the pancreas, but not in its active form as it would digest the pancreatic tissue
Therefore it is synthesised as a slightly longer protein called TRYPSINOGEN
Activation occurs when trypsinogen is cleaved by a protease in the duodenum
Once active, trypsin can activate more trypsinogen
molecules
Slide32Often seen in pathways that involve a series of enzyme controlled reactions.
The end product once produced has an inhibiting affect on an enzyme in the reaction.
Example:
Bacterial production of amino acid isoleucine from threonine.
5 stages enzyme controlled
Threonine Isoleucine
End product Inhibition
Slide33To summarise
As a ligand binds to a protein or a substrate binds to
a
n enzyme’s active site, the conformation of the
protein changes,
This change in conformation causes a functional
change in the protein
.
Slide34To summarise
In enzymes, specificity between the active site and substrate is
related to induced fit.
When the correct substrate starts to bind, a temporary change in
shape of the active site occurs increasing the binding and interaction with the substrate.
The chemical environment produced lowers the activation energy
required for the reaction.
Once catalysis takes place, the original enzyme conformation is
resumed and products are released from the active site.
Slide35To summarise
In allosteric enzymes, modulators bind at secondary binding sites.
The conformation of the enzyme changes and this alters the
a
ffinity of the active site for the substrate.
Positive modulators increase the enzyme affinity whereas
n
egative modulators reduce the enzymes affinity for the substrate.
Slide36Haemoglobin and Oxygen
Slide37Cooperativity in hemoglobin
Deoxyhaemoglobin
has a relatively low affinity for oxygen.
As one molecule of oxygen binds to one of the four
haem
groups in a hemoglobin molecule it increases the affinity of
the remaining three
haem
groups to bind oxygen.
Conversely,
oxyhaemoglobin
increases its ability to loose
oxygen as oxygen is released by each successive
haem
group.
This creates the classic sigmoid shape of the oxygen
dissociation curve.
Slide38Dissociation curve of
haemoglobin
Slide39Deoxyhaemoglobin
Oxyhaemoglobin
Disassociation releasing oxygen to tissues
Association binding oxygen in lungs
Slide40Effects of temperature and pH
Low pH = low affinity.
High temperature = low affinity.
Exercise increases body temperature and produces more
CO
2
, acidifying the blood.
This has a corresponding effect on the
oxyhaemoglobin
dissociation curve.
Slide41Slide42Sickle Cell Anaemia
Low oxygen levels cause
change in haemoglobin
structure.
Strands cause cells to take
o
n bent sickle shape
b
locking capillaries.
Slide43High Altitude and Oxygen
The
concentration of oxygen (O2) in sea-level air is 20.9%, so the
partial
pressure of O2 (pO2) is 21.136
kPa
.
Atmospheric pressure decreases exponentially with
altitude
while the O2 fraction remains constant to
about
100
km, so pO2 decreases exponentially with altitude as
well
.
It
is about half of its sea-level value at 5,000 m
(
16,000
ft
), the
altitude
of the Everest Base Camp, and only
a
third at 8,848 m
(
29,029
ft
), the summit of Mount
Everest. When
pO2 drops, the
body
responds with
altitude
acclimatization
.BBC Horizon How to kill a Human Being
Slide44To summarise
Some proteins with quaternary structure show cooperativity
i
n which changes in binding alter the affinity of the remaining
subunits.
Cooperativity exists in the binding and release of oxygen in
Haemoglobin.
Temperature and pH
influence oxygen association.