Enzymes are biological
catalysts and help speed up reactions, many globular proteins are enzymes. Metabolism which is the sum
of all the chemical reactions occurring in a an organisms. Enzymes control
these metabolic reactions which can either be: -Anabolic = The formation
of molecules from smaller units. -Catabolic= The breaking
down of larger molecules. Activation energy is the amount of energy that is needed for a reaction to start.
An example of this could be
seen in my previous post where I talked about DNA replication and uses the
enzyme DNA Polymerase. Enzymes can intracellular
(work inside cells) or extracellular (work outside cells) like some bacteria
secrete digestive enzymes into the environment to digest their food before
consumption. 1-Substrates collide with the
active site of the enzyme.2-The shape of the active
site is complementary to the substrate.3-The substrate bids to the
active site to form an enzyme-substrate complex (ESC)4-Bonds in the substrate are
placed under strain and break the enzyme provides an alternative reaction
pathway that reduces the activation energy required for the reaction.5-An enzyme product complex
is produced and the products can be released.
The lock-key hypothesis:That the shape of the active
site is a complementary site for the substrate molecule and is therefore
specific to one substrate. The Induced fit hypothesis: When the substrate molecule
binds to the active site it initially has a weak binding by the substrate will
alter the enzyme structure, this strengthens the temporary bonds between the
substrate and the enzyme and weakens the bonds within the substrate.
DNA Replication results in two identical double helices where
genetic information is conserved in each helix and is semi conservative as one strand
is new and one strand is from the original strand.
The genetic code uses a triplet code which is called a codon
and codes for the production of one amino acid. The code is degenerate so means one amino acids
can have many different types of cordons for the same amino acid.
1-DNA unzips by helicase enzyme to create replication fork and
both DNA strands act as a template.
2-Primase enzyme makes a small piece of RNA called primer.
3-DNA polymerase binds to primer and adds bases to 5'-3' end
and the leading strand is made continuously 5'-3' end.
Free monomer nucleotides are activated by phosphate groups are
added to them and free nucleotides form hydrogen bonds with base pairs (A=T) purines
and (C=G) Pyrimidines.
as lagging strand is 3'-5' end primase makes primers every 120
bases to create Okazaki fragments.
Cell signalling is a type of
communication that cells do with one another or with itself. It involves
transmitting ligands which are signalling molecules which then bind to a
receptor protein to create a change such a release a chemical or hormone.
G-Proteins
guanine-nucleotide binding protein.
G-Proteins coupled receptor
structure:
-7 transmembrane alpha
helices with a extracellular N terminus and a cytosolic C terminus containing a
ligland (signalling molecules) binding site also there is a cytosolic loop
between segment 5 and 6 binds specific G proteins.
GPCR (G protein coupled
receptors) are very common types of receptors on the plasma membrane and most
drugs produced work around these types of receptors.
1-Many G protein coupled
receptors have a large extracellular ligland binding domain when an
appropriate protein ligland binds to
this domain the receptor undergoes a conformation change that is transmitted
to its cytosolic regions which now activate a trimeric GTP binding protein also
called g protein.
2-A G protein consists of 3
protein sub units; Alpha beta and Gamma. Alpha and Gamma have contently
attached lipid tails which help anchor the G protein to the membrane, In the
absence of a signal the alpha sub unit has a GDP bound to it and the G protein
is inactive .
3-An activated receptor
induces a conformational change in the
alpha subunit causing the GDP to dissociate and GTP in the cytsol binds in its place
which causes a conformational change activating
both alpha sub unit and beta gamma complex now it can regulate the activity of target
proteins in the plasma membrane
4-The activated target proteins
then relay the signal to other components in the signalling cascade eventually the
alpha sub unit hydrolyses its bound GTP to
GDP which inactivates the sub unit. This is sped up by a protein called RGS (regulator
of g protein signalling). The inactivated alpha sub unit reforms with the beta and
gamma sub units which turns off other downstream events.
5-As long as the signalling receptor
remains stimulated it can continue to activate G proteins but after a very long
time it begins to get inactive. so a receptor kinase phosphorylates the cytosolic
portions of the activated receptor and then binds to a high affinity to arrestin
protein which inactivates the receptor by preventing any interactions with G proteins.
A muscle is an example of an effectors and impulses are
transmitted by motor neurons which stimulate muscle cells to contract and
produce a response.
There are different types of muscles the first one is called
skeletal muscle it has a striated and striped appearance and can be attached to
bones via tendons. The type of contraction is voluntary and is very fast but is
short is in duration. The next is cardiac muscle it is also striated and is
used in the heart and has a involuntary contraction with a intermediate speed
and duration. The next type of muscle is smooth muscle and is non striated and
is used in the blood vessels and digestive system and is involuntary and is
slow and can be long lasting.
Muscle cells fuse to form fibers with each muscle fiber contains many myofibrils and are organelles made principally of having two
proteins called actin and myosin. The myofibrils are then composed of many
repeating units called sarcomeres.
A neuromuscular junction is the synapse between a motor neuron and a muscle fibre and it works
having the principles as a synapse between two neurons and a neurotransmitter
called acetylcholine this diffuses across the synaptic cleft and binds to
receptors on the sarcolemma which results in the depolarisation and a motor
unit comprises all the muscles fibres which is supplied by one motor neurone.
The sliding filament model process
1-The sarcolemma is depolarised
2-The depolarisation spreads through T-tubles to
sarcoplasmic reticulum a specialised smooth endoplasmic reticulum.
3-Calcium ions are released from sarcoplasmic reticulum.
4-Calcium ions binds to troponin which is a protein that is attached
to actin.
5-The troponin changes shape which causes tropomysoin to be moved
away from the myosin binding site it had been covering.
6-Myosin heads bind to the binding site on actin this forms cross
bridges.
7-Myosin heads tilt then moves the actin this is called the power
stroke and ADP is released from myosin at this stage.
8-ATP binds to mysoin causing it to detach from the actin.
9-ATP is hydrolysed to ADP causing the myosin head to resume
its original position the head is free to attach further down the actin and more
than 100 power strokes can be performed by each mysoin each second.
Le Chatelier's principle states
that when any change is made to the conditions of an equilibrium the position of
the equilibrium moves in the direction that minimises the change. Some
reactions are reversible in dynamic equilibrium the rate of forward (right)
reaction is the same as the backward (left) reaction concentrations of products
and reactants stay the same and dynamic equilibrium can only happen in a closed
system Can be any combination of reactants and products, doesn’t have to be
half and half and effects of changes in conditions predicted by Le Chatelier’s
principle.
“If a system at equilibrium is disturbed, the
equilibrium moves in the direction that tends to reduce that disturbance”
Rate of forward or backward reaction increases to minimise
change both forward and reverse rates are speeded up equally and No effect on
the yield . We get no more product, we just get it faster. Industrial equilibrium
use compromise conditions that balance yield against reaction rate, cost and
risks of equipment needed for conditions, side reactions and catalysts. Ammonia,
ethanol and methanol are all produced industrially using a compromise
temperature and pressure
The table below shows some of the properties that occur when
Le chatelier's principle is in use:
The equilibrium constant is the ratio of product concentration
to reactant concentration which is raised to its appropriate power. this only varies
for a reaction when the temperature is changed and it indicates whether the position
of equilibrium to the left or to the right.
The equilibrium constant formula is:
In industry a compromise may be needed between yield and rate
such as for exothermic reaction, a lower
temperate gives you a higher yield and a lower temperature saves costs in terms
of no need to pay for electricity to create heat or fuel on the other hand a lower
temperature slows down the forward backward reactions so it would take longer to
reach equilibrium.
Measurements of lung function tend to be made using two pieces
of equipment called a peak flow meter and/or a spirometer.
A peak flow meter measures the
rate at which a patient expel air into a handheld tube, this can be used to monitor
conditions such as asthma.
A spirometer is where patients
breathe in and out of a mouthpiece attached to a sealed chamber where oxygen from
the chamber is used up this can be used to measure many different lung components
when a pencil attached to a rotating drum can create a trace on a spirometry graph
paper.
Total lung capacity:
Vital capacity + residual volume
Residual volume: is
the volume remaining in the lungs even after a person has exhaled with maximum force.
Vital capacity: is
the maximum volume that can be breathed out following the strongest possible inhalation
(i.e. tidal volume + inspiratory reserve volume + expiratory reserve volume)
Tidal Volume: is
the volume inhaled with each resting breath (or the volume exhaled with each resting
breath)
Inspiratory and expiratory reserve volumes are the additional volumes of air that can be breathed in
and out during forced inhalation and exhalation.
vital capacity can potentially
be defined and measured in two ways it can either the maximum volume of air exhaled
following the strongest possible inhalation or the maximum volume inhaled following
the strongest possible exhalation and both values should be the same.
Breathing rate=The number of
breath per minute.
Ventilation rate= The total volume
inhaled per minute=Breathing rate X Tidal volume
The electron transport chain is located on the inner
mitochondrial membranes. The chains use energy from electrons to pump H+ ions
into the intermembrane space. A proton gradient is established which enables
chemiosmosis to occur through ATP synthasae. The sequence of events is as
follows:
Most of the ATP generated
in respiration is produced via oxidative phosphorylation. The reduced
coenzymes FADH2 and NADH produced during
the earlier stages of respiration such as glycolysis donate H+ ions and
electrons to an electron transport chain and ATP is synthesised.
There are 5 complex called :
Complex 1-NADH Dehydrogenase
Complex 2-Succinate Dehydrogenase
Complex 3-Cytochrome C reudctase
Complex 4-Cytochrome C oxidase (a-a3 Complex)
Complex 5-F0-F1
Mobile carriers:
Q= Ubiquinone
Cyt C=Cytochrome C
Let's talk about NADH the first product made from glycolysis. It transfers h+ and E- electrons
into Complex 1 to Q a mobile carrier and then to complex 3 to Cyt C another
mobile carrier to complex 4 where the electron is accepted by oxygen with
hydrogen to make water. All this movement from the electron carriers complexes
have created energy this energy is used to pump hydrogen ions into the
intermembrane space which create a proton gradient this then means that H+ ions
can enter back into the matrix this is done by complex 5 and this then causes ADP
to hydrolysis with Phosphate to create ATP.
For every 2H+ion 1 ATP is created
altogether the 6 H+ ions creates 3 ATP
Now let's talk about the second product used from glycolysis
called FADH2, it takes a slightly different pathway. FADH2 is oxidised to FAD+ in
complex 2 and enter Q mobile carrier where electrons travel to complex 3 and then
to Cyt C mobile carrier and then to complex 4 where electrons get accepted to oxygen
and hydrogen to produce water, H+ ions pump from complex 3 and complex 4 and this
creates a proton gradient where H+ ions enter back via complex 5 which creates ATP.
-4H+ ions can produce 2 ATP
Overall this how much energy is created from oxidative phospohorylation:
ATP
NADH/FADH2
ECT ATP produced
Glycolysis
4
2 NADH
6
Link Reaction
------
2 NADH
6
TCA Cycle
2
6 NADH
2 FADH
18
4
Total:
6
34
Total: 6+34=40 ATP
*Net gain ATP: 40-2=38
*Hint: 2 ATP was used in the beginning of glycolysis.*
Linoleate (18) and 3 double bonds, Arcahedonate (20) has 4
double bonds.
Unsaturated fatty acids in membranes are in cis creating
beds and kinks so do not pack tightly in membrane.
Movement of phospholipids within membranes.
-Rotation
-Lateral diffusion
-Transverse diffusion (flip-flop): this is where one
monolayer to another and is done by proteins in ER called phospholipids translocations
and flippases enzymes.
Lipid membrane is fluid which allows lateral diffusion and
move faster than proteins are smaller and weigh less.
Florescence recovery after photo bleaching
1-unlabbled cell surface
2-cell surface molecules labelled with fluoresce dye
3-laser beam bleaches an area of cell surface
4-Florucescent labelled molecules diffuse into bleached
area.
Dye creates covalent bond to
living cell.
-->Uses a high intensity
laser beam
-->Rate of diffusion
florescence into bleached area measured over time.
Temperature changes
fluidity:
transition temperature (Tm)=
Temperature when it melts
Phase transition= Membrane
changes state.
Differential scanning calorimetery
-''n''' shaped curve
-Peak is the Tm
-More saturated the higher
temperature
saturated fatty acids fit more
tightly packed as there are no bends.
Determining fluidity:
-length of fatty acid chains
(long chains higher temperature) less fluid.
-Degree of unstauration
Some more in depth information
into cholesterol:
-Sterols affect membrane fluidity
-PH group that is polar and everything
else hydrophobic
-forms hydrogen bond
-Rigid hydrophobic steroid rings
and hydrocarbon chain part interact with adjacent hydrocarbon chain that are adjacent
to closest phospholipids head group.
-Plant cholesterol is phytosterols
-Sterol is hopanoids in prokaryotes
-Decrease membrane fluidility
above Tm
-Increase membrane fluidilty
below Tm
Sterols decrease permeability
of lipid bilayer of ions and smaller polar molecules
Pilikotherms (cold blooded animals)
cannot regulate own temperature as lipid fluidity decreases as temperature falls
membrane would gel. Homotherms (warm blooded) animals compensating effects such
as when cold and when you can't feel fingers and toes as sensory never ending stop.
When very hot pilikiotherms membranes get very fluid and denature homeoviscous adaptation
also is the regulation of membrane fluidility.
Lipid rafts are newly discovered
and are localised regions of membrane lipid that are involved in cell signalling.
Glycolysis is the simply the
process of breaking down a sugar such as Gluclose into energy and pyruvate.
The chemical equation for
respiration is:
C6H12O6 +
6O2 ==> 6CO2 + 6H20
+ ATP
Glucose Oxygen Carbon dioxide Water Energy
the main stages of
glycolysis are:
Stage One:
To trap the glucose in the cell and destabilise it structure.
Stage Two:
To break down the glucose into smaller components.
Stage Three:
Harvest the energy to form ATP molecules and pyruvates.
As this topic is very
complicated and difficult to make it simpler with less rambling. I am going to
break glycolysis into ten simple steps!
STEP ONE:
The phosphorylation of
glucose, glucose moves into the cell with the help of a membrane transporter
and once inside the cytoplasm it undergoes phosphorylation process that is
catalysed by protein kinases called hexokinase.
This step is important as:
-Makes glucose polar which
traps the glucose into the cell.
-The negatively charged
phosphate group stops the glucose from moving across the cell membrane.
-The addition of a charged
moiety on the glucose destabilises the structure and increases its energy which
makes it more reactive and more likely to undergo glycolysis.
Some information on the
enzyme hexokinase:
-Hexokinase depends on the
presence of a divalent metal atom such as Mg2+
-Glucose moves into the
active site of hexokinase which creates a induced fit, which seals off water
out and stops ATP from being hydrolysed and it also places the glucose sugar
more closer to the ATP.
STEP 2:
Enzyme phosphogluclase
isomerase transforms on aldose (glucose 6 phosphate) into a ketose (fructose 6
phosphate)
STEP 3:
The OH group on carbon one
of fructose 6 phosphate is phosphorylised by ATP and catalysed by PFK enzyme.
Phosphofructokinase (PFK)
adds a second phosphoryl group on the sugar which commits the sugar to
glycolysis.
STEP 4:
Here we can see the
breakdown of gluclose into smaller components. The aim of stage 2 is to cleave
the fructose 1,6 bisphosphat inot two 3 carbon molecules called Glyceraldehyde
3- phosphate (GAP).
An enzyme called aldolase
catalyse the breakdown of fructose 1.6 bisphosphate into two different 3 carbon
moleculates called glyceraldehyde 3 phosphate and Dihydroxyacetone phosphate
(DAP)
The glyceraldehyde lies directly
on the glycolysis pathway which means it can go directly onto stage 3 of
glycolysis without any problems, however Dehydroxyacetone phosphate (DAP) does
not so needs to be modified. To prevent the loss of energy potential the DAP
must to be converted to GAP.
STEP 5:
An enzyme called triose
phosphate isomerase catalyse the rapid and reversible conversion of DAP to GAP.
TPI catalyses the conversion
of the ketose (DAP) into aldose (GAP) via an intermolecular redox reaction in
which a hydrogen is transferred from carbon one to carbon 2.
STEP 6:
This is stage three where glycolysis aims to harvest the energy in
glyceraldehyde 3 phsophate to form ATP, NADH and pyruvate molecules.
The initial process involves
the conversion of the glyceraldehyde 3 phsophate (GAP) into 1.3 Bisphoglycerate
this reaction is catalysed by anenzyme called Glyceradlehyde 3 phosphate
dehydrogenase.
STEP 7:
The transfer to ADP of the high
energy phosphate group that was generated in step 6 to make ATP. It is catalysed by the enzyme phosphoglycerate
kinase.
STEP 8:
The left over phosphate ester
linkage in 3 phosphoglycerate which has a very low free energy of hydrolysis is
moved to carbon 2 from carbon 3 to create 2 phosphoglycerate.
It is catalysed by the enzyme
phosphoglycerate mutase.
STEP 9:
The removal of water from 2 phosphoglycerate
which creates a high energy enol phosphate linkage. It is also catalysed by enolase
enzyme.
STEP 10:
The transfer to ADP of the
high energy phosphate group that was generate in step 9 creates glycolysis.
This is catalysed by the pyruvate kinase enzyme.
The whole process:
TIP: ... and that is it! Learning this the first time
round can be quite tricky! From all the diagrams and names it does look
puzzling but with practice and going over it a number of time you will get the
hang of it! I personally found this topic the hardest in biology and I have
written the notes in a very simple and concise way! I have attached a
additional video which I have found useful in understanding this topic.
Chromatography is the process of separating a mixture by passing it into a solution where its components
move at different rates.
Chromatography is a technique that can be used for a wide
range of chemistry and biological processes, but for now I will tell you about
thin layer chromatography in terms of membrane proteins and separating its
lipid components that the membrane contains.
1-Sample is spotted this is called the origin and left to
dry on a glass or metal plated this is covered in a layer of silicic acid.
2-Sample components are carried up the plate by the solvent
and due to the capillary action.
3-Lipid components separate due to polarity differences.
4-more polar substances is down the plate whilst less polar
substances are up the plate.
In the next few blogs we will be discussing more about membrane proteins.
Gaseous exchange: is the
transfer of oxygen from the air into the blood and carbon dioxide in the blood
to the air.
The gaseous exchange
system has to keep a balance in providing gaseous exchange and making sure not
too much water is lost from the body.
This is what the main
gaseous exchange system looks like:
Nasal Cavity: warms air that
enters the body and can trap dust and bacteria which protects the body from
diseases, hairy nose hairs warm air breathed in to body temperature (37◦) this
also reduced evaporation from the lungs by limiting the concentration gradient
for diffusion to occur.
The main features of the
nasal cavity is that it has good blood supply and lined with hairs and mucus
secreting hairs called epithelial and goblet cells respectively).
Trachea: Prevents the collapse of the respiratory system and traps
dust and bacteria and has cilia which sweeps mucus and dust away from the
lungs.
-It is supported by flexible
rings of incomplete rings of cartilage and lined with goblet cells and ciliated
epithelium cells.
Bronchus: very similar to the trachea made from incomplete rings of
cartilage and helps prevent collapse of the system.
Bronchioles: Are able to
constrict and dilate (become smaller and
wider) so to control the amount of the air reaching the lungs.
-Capable of doing some
gaseous exchange and contains smooth muscles
with no cartilage and flattened epithelium cells.
Alveoli: A very important part of the system where most of the
gaseous exchange happens, it is a small sac very much like a balloon.
provides a short diffusion
pathway which increases the diffusion rate due to the single layer of flattened
epithelium cells.
contains elastic fibers and collagen which enables the stretching and elastic recoil during ventilation
this can help increase the amount of air that can breathed in and stops it from
bursting.
Alveoli have large surface
areas which can increase the rate of diffusion and has a good blood supply as
many capillaries are very close by which provide a steep concentration of very
high deoxygenated blood and very rich oxygenated blood coming together so the
exchange can happen very quickly.
alveoli is covered with a layer of surfactant which stop
the alveoli from collapsing and keeps it remained open.
Here is what a Alveoli
looks like: note that there are many
thousands of alveoli in the lungs possibly millions!
Ventilation: Air that
moves in and out of the lungs.
Ventilation happens
because of changes in pressure ventilation helps us have a steep concentration
gradient in the lungs of low and high oxygen concentration which allows for
very fast gaseous exchange.
There are two types of
ventilation called inhalation and expiration more commonly known as breathing
in and out.
the steps of how each
process occurs is written below:
Inspiration (Inhalation- breathing in)
1-External intercostal
muscles contract
2-Ribs move up and out
3-Diaphragm contracts and
flattens
4-Throax volume increases
5-Air pressure in the
lungs lower
6-Air moves into the lungs
Expiration (Exhalation-breathing out)
1-External intercostal muscles
relax
2-Ribs move down and in
3-Diaphragm relaxes and
goes to being domed shaped
4-Throax volume decreases
5-Air pressure rise
6-Air moves out of lungs
TIP: As you may have noticed that Inspiration is the opposite of Expiration
so it may be easier to just learn one and just write the opposite if needed when
it comes to the exams.
Inspiration is a active process
which means it needs energy but Expiration at rest is passive and does not require
energy. However forceful expiration does require energy such as when you are coughing.
