Download Advanced Higher Cells and Proteins

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?
Why is protein structure important in relation to its function?
DNA AND PROTEINS
This lesson will cover
• DNA and its
associated proteins
• Other proteins
involved with
transcription
DNA AND PROTEIN ASSOCIATION
DNA 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.
DNA AND PROTEIN ASSOCIATION
Animation
HISTONE PROTEINS AND NUCLEOSOME
OTHER 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
DNA AND PROTEIN COMPLEX IN TRANSCRIPTION
TRANSCRIPTION 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.
TRANSCRIPTION 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.
BINDING 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.
BINDING 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.
Enzymes
All 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.
Anabolic Reactions
• Uses energy to SYNTHESISE
large molecules from smaller
ones e.g.
Amino Acids
Proteins
• Also known as endothermic
reactions
ENDOTHERMIC REACTION
Catabolic 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
Enzyme types
Proteases - break down proteins into amino acids
by breaking peptide bonds (hydrolysis).
Nucleases - break down nucleic acids into
nucleotides (hydrolysis).
Kinases - add phosphate groups to molecule.
Phosphatases – remove phosphate groups
ATPases - hydrolysis of ATP.
Control 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
How do enzymes work?
Induced 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
Competitive inhibition
A 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.
Malonate example
Succinate dehydrogenase catalyses the oxidation of
succinate to fumarate (respiration)
Malonate is the competitive inhibitor
Non-competitive inhibition
An 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.
•Inhibition 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.
Enzyme modulators
Some 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.
Allosteric Enzymes
Covalent modifications
Involves 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
An example of activation is trypsinogen to trypsin
trypsinogen activated by
enterokinase in duodenum
Trypsin 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
End product Inhibition
Often 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
To summarise
As a ligand binds to a protein 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.
To 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.
To summarise
In allosteric enzymes, modulators bind at secondary binding sites.
The conformation of the enzyme changes and this alters the
affinity of the active site for the substrate.
Positive modulators increase the enzyme affinity whereas
negative modulators reduce the enzymes affinity for the substrate.
Haemoglobin and Oxygen
COOPERATIVITY 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.
DISSOCIATION CURVE OF HAEMOGLOBIN
Disassociation releasing oxygen to tissues
Deoxyhaemoglobin
Oxyhaemoglobin
Association binding oxygen in lungs
EFFECTS OF TEMPERATURE AND PH
• Low pH = low affinity.
• High temperature = low affinity.
Exercise increases body temperature and produces more
CO2, acidifying the blood.
This has a corresponding effect on the oxyhaemoglobin
dissociation curve.
Sickle Cell Anaemia
Low oxygen levels cause
change in haemoglobin
structure.
Strands cause cells to take
on bent sickle shape
blocking capillaries.
HIGH 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
To summarise
Some proteins with quaternary structure show cooperativity
in 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.