Unit 1 from PPQs Flashcards
amino acids in the membrane are hydrophobic/hydrophilic
Hydrophobic
amino acids out of the membrane are hydrophobic/hydrophilic
hydrophilic
only target cells respond to a signal molecule because..
only target cells have receptor molecules for signalling molecules
what is ensured by having only target cells having receptor molecules for signalling molecules
only target cells will respond to a signal
order of cell cycle stages
G1 - S - G2 - M
what is p53 involved in
cell cycle arrest, DNA repair, apoptosis
what protein is involved in cell cycle arrest, DNA repair, apoptosis
p53
structure of spindle fibres
spindle fibres are made of microtubules
spindle fibres are composed of hollow tubes made of tubulin
cell division requires remodelling of cytoskeleton
spindle fibres in mitosis (4)
radiate from the centrosome
attach to chromosomes
spindle fibres contract
and separate chromatids
function of NaK pump
maintaining osmotic balance
generation of ion concentration gradient for glucose symport
generation of ion concentration gradient in kidney tubules
Generates and maintains resting potential in neurons
what maintains osmotic balance
and
generates of ion concentration gradient for glucose symport, and maintenance of resting potential
function of NaK pump
role of ATP in altering the affinity of NaK pump for sodium ions
ATP binds to pump and conformational change of the pump occurs
This lowers the affinity of the pump for Na+ ions
What happens when a competitive inhibitor binds to K+ attachment site on NaK pump
Prevent binding of K+ ions
Preventing de-phosphorylation
What can arise from a uncontrolled decrease in the rate of cell cycle
Degenerative disease
What can degenerative disease arise from
Uncontrolled decrease in the rate of cell cycle
Mitosis phases in order
Prophase
Metaphase
Anaphase
Telophase
What forms photoreceptor proteins
Light sensitive molecule retinal and opsin
.
.
How is sensitivity achieved in cells
High degree of amplification
What does a high degree of amplification allow for
Light sensitivity
What extra wavelength are birds sensitive to
UV
How does a hydrophobic hormone molecule cause an effect within target cell
The hormones diffuses through the cell membrane
It binds to receptors which switches transcription on/off
Why can a signalling molecule have different effects in different tissues
Different tissues will have different responses to receptor binding
Why can a signalling molecule have different effects in different tissues
Different tissues will have different responses to receptor binding
Where are hydrophilic R groups of a soluable protein
Mostly at the surface
Where are soluble protein found
Cytoplasm
Hydrophobic groups of insoluble proteins might do what
Cluster at centre of protein
What may cluster at the centre of a protein in soluble proteins
Hydrophobic groups
Membrane proteins can be what
Integral or peripheral
What can be integral or peripheral
Membrane proteins
Some integral proteins are what
Transmembrane
Example of transmembrane integral proteins
Channels
Transporters
Receptors
Channels
Transporters
Receptors
Are examples of..
Integral transmembrane proteins
R group interactions in integral proteins
Hydrophobic R groups interact with hydrophobic region of membrane
Hydrophilic R groups interact with extraneous environment
Hydrophobic R groups interact with hydrophobic region of membrane
Hydrophilic R groups interact with extraneous environment
Integral membrane
R group interactions of peripheral proteins
Hydrophilic R groups interacting with hydrophilic heads of phospholipids
Is the membrane hydrophobic or hydrophilic
Has hydrophobic and hydrophilic regions
What can’t cross the membrane
Polar substances
What can cross the membrane
Non polar substances
Oxygen, water and carbon dioxide can/came pass through the membrane
Can
What are needed for charged substances to pass the membrane
Protein channels, pumps, and transporters
What do transporter proteins do
Control ion concentrations
What type of transport is channels
Passive
Transporter proteins changing
Change conformation to transport molecules across the membrane
What changes conformation to transport molecules across the membrane
Transporter proteins
Conformation change on active transport requires…
Energy from hydrolysis of ATP
What are ligand gated channels opened/closed by
Binding of signal molecules
Voltage gated channels are controlled by what
Changes in ion concentrations
GLUT4 function
Transports glucose in fat cells
integral protein
found within membrane
found within membrane
integral protein
the head of phospholipid is…
polar
the tail of phospholipid is…
non polar
peripheral proteins are found where
on the surface of the membrane
what part of phospholipids do integral proteins interact with
Hydrophilic head
transmembrane
protein spans across the entire width of the membrane
peripheral membrane proteins have what on their surface
hydrophilic R groups
how are peripheral proteins bound to the surface of membranes
mainly by ionic and hydrogen bonds
facilitated diffusion
passive transport of substances across the membrane through specific transmembrane proteins
passive transport of substances across the membrane through specific transmembrane proteins
facilitated diffusion
what allow for facilitated diffusion
channel proteins and transporter proteins
channel proteins
multisubunit proteins with subunits arranged to form water filled pores that extend across the membrane
multisubunit proteins with subunits arranged to form water filled pores that extend across the membrane
channel proteins
how do transporter proteins work
bind to specific substances to be transported and undergo a conformational change to transfer molecule across the membrane
bind to specific substances to be transported and undergo a conformational change to transfer molecule across the membrane
transporter proteins
pump proteins use what transport
active transport
what do pump proteins require
energy
ATPases do what
hydrolyse ATP
what hydrolyse ATP
ATPases
what does the electrochemical gradient of a solute determine
the transport of the solute
electrochemical gradient
concentration gradient and electrical potential gradient combine to form this
membrane potential
when there is a difference in the electrical charge, created when there is a different between the two sides of the membrane
membrane potential
when there is a difference in the electrical charge, created when there is a different between the two sides of the membrane
what are the charges of inside and outside the cell?
net negative charge inside the cell
net positive charge outside the cell
what does the NaK pump in and out of the cell
3 sodium ions out of the cell
2 potassium ions into the cell
NaK pump steps (6)
the pump has a high affinity for sodium ions in the cell
binding occurs and the pump is phosphorylated by ATP
conformation of the protein changes. the affinity for sodium ions decreases, they are released out of the cell
potassium ions bind outside of the cell
dephosphorylation occurs and the conformation of the protein changes
potassium ions are brought into the cell and the original affinity is restored
how do multicellular organisms signal between cells
with extracellular signalling molecules
eg steroid hormones, peptide hormones, neurotransmitters
receptor molecules/target cells
proteins with a binding site for a specific signalling molecule
what happens when a signalling molecule binds to a receptor
changes the conformation of the receptor, causing a response within the cell
signalling molecules effect
may have different effects on different target cell types due to differences in the intracellular signalling molecules and pathways that are involved
hydrophobic signalling molecules and the membrane
diffuse directly through the phospholipid bilayers of the membrane and bind to intracellular receptors
diffuse directly through the phospholipid bilayers of the membrane and bind to intracellular receptors
hydrophobic signalling
what are hydrophobic signalling molecules receptors called
transcription factors
transcription factors
proteins that, when bound to DNA, can either stimulate or inhibit the initiation of transcription
proteins that, when bound to DNA, can either stimulate or inhibit the initiation of transcription
transcription factors
examples of hydrophobic signalling molecules
oestrogen and testosterone, steroid hormones
where to steroid hormones bind to
specific receptors in the cytosol or the nucleus
what happens when hydrophobic molecules bind to receptor
the hormone receptor complex moves to the nucleus where it binds to specific sites on DNA and affects gene expression
when does the hormone receptor complex moves to the nucleus where it binds to specific sites on DNA and affects gene expression
when the hormone binds to the receptor
effect of hydrophobic signalling
binds to specific sites on DNA and affects gene expression
binds to specific sites on DNA and affects gene expression
hydrophobic signalling
what do hormone receptor complex bind to on DNA
specific DNA sequences called hormone response elements (HRE)
what happens when hormone receptor complex binds to HREs
influences the rate of transcription with each steroid hormone affecting the gene expression of many different genes
what influences the rate of transcription with each steroid hormone affecting the gene expression of many different genes
binding of hormone receptor complex to HRE
what do hydrophilic signalling molecules bind to
transmembrane receptors
do not enter the cytosol
transmembrane receptors
do not enter the cytosol
hydrophilic signalling molecules
examples of hydrophilic signalling molecules
peptide hormones and neurotransmitters
peptide hormones and neurotransmitters
hydrophilic signalling molecules
what happens when ligands bind to the extracellular face of transmembrane receptors
the receptors change conformation
the signal molecule does not enter the cell but the signal is transduced across the plasma membrane
what do transmembrane receptors act as
signal transducers
how do transmembrane receptors act as signal transducers
by converting the extracellular ligand binding event into a intracellular signals which alter the behaviour of the cell
what do transduced hydrophilic signals often involve
G proteins or cascades of phosphorylation by kinase enzymes
G proteins or cascades of phosphorylation by kinase enzymes
transduced hydrophilic signals involve
G proteins
relay signals from activated receptors (receptors that have bound to a signalling molecule) to target proteins such as enzymes and ion channels
relay signals from activated receptors (receptors that have bound to a signalling molecule) to target proteins such as enzymes and ion channels
G protein
phosphorylation cascades
one kinase activating the next in the sequence and so on
one kinase activating the next in the sequence and so on
phosphorylation cascades
insulin as an example of cascades of phosphorylation
the binding of the peptide hormone insulin to its receptor results in intracellular signalling cascades that triggers the recruitment of the GLUT4 glucose transporter proteins to the cell membrane of fat and muscle cells
what is diabetes caused by
type 1 - failure to produce insulin sufficiently
type 2 - loss of receptor function
how to help with type 2 diabetes
exercise triggers recruitment of GLUT4
this can improve the uptake of glucose to fat and muscle cells
treatment for type 1 diabetes
daily insulin injections
nerve impulse
signal transmitted along a nerve fibre
signal transmitted along a nerve fibre
nerve impulse
resting membrane potential
no net flow of ions across the membrane
no net flow of ions across the membrane
resting membrane potential
what does the transmission if a nerve impulse require
changes in the membrane potential of the neurons plasma membrane
action potential
wave of electrical excitation along a neurons plasma membrane
wave of electrical excitation along a neurons plasma membrane
action potential
depolarisation
sudden change in the membrane potential
usually from a relatively negative to positive internal charge
sudden change in the membrane potential
usually from a relatively negative to positive internal charge
depolarisation
why does depolarisation happen
entry of positive ions, triggering the opening of voltage gated sodium channels and further depolarisation occurs
repolarisation
inactivation of the sodium channels and the opening of potassium channels restores the resting membrane potential
inactivation of the sodium channels and the opening of potassium channels restores the resting membrane potential
repolarisation
effect of neurotransmitters
triggers the opening of ligand gated ion channels at a synapse
ion movement occurs and there is a depolarisation between of the plasma membrane. if sufficient ion movement occurs, and the membrane is depolarised beyond a threshold value, the opening of voltage-gated sodium channels is triggered and sodium ions enter the cell down their electrochemical gradient
this leads to a rapid and large change in membrane potential. a short time after opening, sodium channels become inactivated. voltage gated potassium channels then open to allow potassium ions to move out of the cell and restore resting membrane potential
triggers the opening of ligand gated ion channels at a synapse
binding of neurotransmitters
what happens when ion movement occurs
there is depolarisation of plasma membrane
generation of action potential (5)
a stimulus starts the rapid change in voltage or action potential. this must reach above a threshold voltage to start membrane depolarisation
depolarisation caused by a rapid rise in membrane potential opening of the sodium channels in the cellular membrane. this results in a large influx of sodium ions
membrane repolarisation results from rapid sodium channel inactivation as well as a large efflux of potassium ions resulting from activated potassium channels
hyper polarisation - lowered membrane potential caused by the efflux of potassium ions and closing of potassium channels
resting state is when the membrane potential returns to resting voltage that occured before the stimulus occurred
depolarisation of a patch of membrane causes what
neighbouring regions to depolarise and go through the same cycle as adjacent voltage gated sodium channels are opened
what happens when action potential reaches the end of the neuron
vesicles containing neurotransmitters to fuse with the membrane
the neurotransmitter is released and stimulate a response in a connecting cell
cytoskeleton
gives mechanical support and shape to cells
consist of different protein structures including microtubules which are found in all eukaryotic cells
gives mechanical support and shape to cells
consist of different protein structures including microtubules which are found in all eukaryotic cells
cytoskeleton
microtubules
hollow cylinders composed of the protein tubulin
they radiate from the centrosome
hollow cylinders composed of the protein tubulin
they radiate from the centrosome
microtubules
what do microtubules control
the movement of membrane bound organelles and chromosomes
what controls the movement of membrane bound organelles and chromosomes
microtubules
what does cell division require
remodelling of the cytoskeleton
what do microtubules form from
the spindle fibres that are activate during cell division
what does the formation and breakdown of microtubules involve
polymerisation and depolymerisation of tubulin
Hazard
Any source of potential damage, harm or adverse health
Any source of potential damage, harm or adverse health
Hazard
Risk
The likelihood of harm arising from exposure to a hazard
The likelihood of harm arising from exposure to a hazard
Risk
Control measures examples
Appropriate handling techniques
Protective clothing and equipment
Aseptic techniques
Linear dilution
Range of dilutions that differ by an equal interval
Range of dilutions that differ by an equal interval
Linear dilution
Log dilution
Range of dilutions that differ by a constant proportion
Range of dilutions that differ by a constant proportion
Log dilution
Linear dilution method
Different volumes of stock solutions added to different solvents
Each concentration is made individually and any measurement errors affects only one concentration
Different volumes of stock solutions added to different solvents
Each concentration is made individually and any measurement errors affects only one concentration
Linear dilution
Log dilution
Each dilution acts as the stock for the subsequent dilution
Earlier measurement errors are compounded in later dilutions
Each dilution acts as the stock for the subsequent dilution
Earlier measurement errors are compounded in later dilutions
Log dilution method
Standard curve
Plot known measurements on a graph and use the line to determine an unknown value
Plot known measurements on a graph and use the line to determine an unknown value
Standard curve
Buffer
Solution where adding acids or alkalis has a small effect on pH. This allows pH in a reaction mixture to be kept constant
Solution where adding acids or alkalis has a small effect on pH. This allows pH in a reaction mixture to be kept constant
Buffer
Colorimeter use
Quantify concentration and turbidity
What quantifies concentration and turbidity
Colorimeter
What to do before using colorimeter
Calibrate before use with a blank sample to provide a baseline reading
Calibrate before use with a blank sample to provide a baseline reading
Before using colorimeter
How does colorimeter work
Light is split into its component colours are filtered so there is one wavelength of light
This is passed through the sample solution where a detector picks up how much light has been absorbed or transmitted
Light is split into its component colours are filtered so there is one wavelength of light
This is passed through the sample solution where a detector picks up how much light has been absorbed or transmitted
Colorimeter
What can absorbance be used to determine
Determine concentration of a coloured solution using suitable wavelength filters
Determine concentration of a coloured solution using suitable wavelength filters
Using a colorimeters absorbance reading
What can a colorimeters percentage transmission be used to determine
Turbidity, such as cells in suspension
Higher transmission = less turbid
How can you calculate turbidity
Measuring transmission with colorimeter
What does a centrifuge do
Separate material according to density
What separates material according to density
Centrifuge
Supernatant
Less dense components remain in liquid
Less dense components remain in liquid
Supernatant
Pellet
More dense components stay here
More dense components stay here
Pellet
What can chromatography separate based on
Substances such as amino acids and sugars
What can separate substances such as amino acids and sugars
Chromatography
In chromatography, does the differing solubility in the solvent used determine
The speed each solute travels along the chromatogram
The speed each solute travels along the chromatogram is based on
The differing solubility in the solvent used
Paper chromatography overview
Simple process involving a strip of chromatography paper
Simple process involving a strip of chromatography paper
Paper chromatography
Thin layer chromatography overview
Thin layer of absorbent silica gel over a slide of glass
Advantages of TLC compared to paper chromatography
Runs faster
Gives better separations
Thin layer of absorbent silica gel over a slide of glass
Thin layer chromatography
Rf value calculation
Distance from origin to top of pigment / distance from origin to top of solvent
Distance from origin to top of pigment / distance from origin to top of solvent
Rf value
What is affinity chromatography used to separate
Proteins
Affinity chromatography (4)
A solid matrix or gel column is created with specific molecules (usually receptors) bound to the matrix or gel
Soluble target proteins in a mixture with a high affinity for these molecules become attached as the mixture passes down the column
Other non target molecules with a weaker affinity are washed out
Target proteins can then be removed from the receptors and retrieved
A solid matrix or gel column is created with specific molecules (usually receptors) bound to the matrix or gel
Soluble target proteins in a mixture with a high affinity for these molecules become attached as the mixture passes down the column
Other non target molecules with a weaker affinity are washed out
Target proteins can then be removed from the receptors and retrieved
Affinity chromatography
What can gel electrophoresis be used to separate
Proteins and nucleic acids
What separates proteins and nucleic acids
Gel electrophoresis
Gel electrophoresis method
Charged macromolecules move through an electric field applied to a gel matrix
Samples are loaded into wells in a gel and an electric current is ran through it. Charged molecules will love towards the opposite charge.
Smaller molecules travel faster than larger molecules so will travel further
two forms of gel electrophoresis
native gel
SDS PAGE
what does native gel separate based on
molecules by shape, size and charge
separating molecules by shape, size and charge
native gel
what does SDS page separate based on
size alone
what separates molecules by size alone
SDS page gel electrophoresis
effect of native gel on molecule
they do not denature the molecule
so it can be separated based on shape, size and charge
what gel electrophoresis doesn’t denature the protein
native gel
how does SDS PAGE gel electrophoresis work
gives all molecules an equally negative charge and denatures them
what gives all molecules an equally negative charge and denatures them
SDS PAGE gel electrophoresis
isoelectric point (IEP)
the pH at which a soluble protein has no net charge and will precipitate out of a solution
the pH at which a soluble protein has no net charge and will precipitate out of a solution
IEP
separating based on IEP
if a solution is buffered to a specific pH, only the protein(s) that have an IEP of that pH will precipitate.
if a solution is buffered to a specific pH, only the protein(s) that have an IEP of that pH will precipitate.
separating proteins based on IEP
what can IEP be used alongside
gel electrophoresis
using IEP and gel electrophoresis together
proteins migrate towards the charges until they reach an area with the pH of their IEP
a protein stops migrating through the gel at its IEP in the pH gradient because it has no net charge
proteins migrate towards the charges until they reach an area with the pH of their IEP
a protein stops migrating through the gel at its IEP in the pH gradient because it has no net charge
using IEP and gel electrophoresis together
immunoassay technique
used to detect and identify specific antibodies
used to detect and identify specific antibodies
immunoassay techniques
what do immunoassay techniques use
stocks of antibodies with the same specificity, known as monoclonal antibodies
stocks of antibodies with the same specificity
monoclonal antibodies
what is an antibody specific to the protein antigen linked to
a chemical label
what is a chemical label linked to
an antibody specific to the protein antigen
what is a chemical label
often a reporter enzyme producing a colour change but chemiluminescence, fluorescence and other reporters can be used
often a reporter enzyme producing a colour change but chemiluminescence, fluorescence and other reporters can be used
chemical label
what does an immunoassay using a specific antigen detect the presence of
antibodies to test diseases
what does each antibody bind to
a specific antigen
what binds to a specific antigen
antibody
each _____ binds to a __________
antigen/antibody, antigen/antibody
each antibody binds to a specific antigen
what can antibodies be used for in immunoassay techniques
detecting a target antigen
antigens and antibodies in immunoassay techniques
antibodies can be used to detect a target antigen
ELISA
analytical technique which uses antibodies to detect the presence of an antigen in a solution
analytical technique which uses antibodies to detect the presence of an antigen in a solution
ELISA
when is western blotting used
after SDS PAGE gel electrophoresis
what can you do after SDS PAGE gel electrophoresis
western blotting
western blotting method (2)
the separated proteins from the gel are transferred onto a solid medium
the proteins can be identified using specification antibodies that have reporter enzymes attached
the separated proteins from the gel are transferred onto a solid medium
the proteins can be identified using specification antibodies that have reporter enzymes attached
western blotting method
bright field microscopy
used to observe whole organisms, parts of organisms, or thin sections of dissected tissue and individual cells
used to observe whole organisms, parts of organisms, or thin sections of dissected tissue and individual cells
bright field microscopy
thickness of tissue when doing bright field microscopy
must be thin enough for light to pass through
fluorescence microscopy
uses specific fluorescent labels to bind to, and visualise, certain molecules or structures within cells or tissues
uses specific fluorescent labels to bind to, and visualise, certain molecules or structures within cells or tissues
fluorescence microscopy
purpose of aseptic technique
eliminate unwanted microbial contaminants when culturing microorganisms or cells
what eliminates unwanted microbial contaminants when culturing microorganisms or cells
aseptic technique
what does aseptic technique involve
the sterilisation of equipment and culture media by heat or chemical means
and
subsequent exclusion of microbial contaminants
what can a microbial culture be started with
an inoculum of microbial cells on an agar medium
or
in a broth with suitable nutrients
what can be started with…
an inoculum of microbial cells on an agar medium
or
in a broth with suitable nutrients
a microbial culture
what must animal cells have added to their growth medium
growth factors from serum
growth factors
proteins that promote cell growth and proliferation
proteins that promote cell growth and proliferation
growth factors
what cells need growth factors
animal cells
two forms of cells
primary cell lines
tumour cell lines
primary cell lines
can divide a limited number of times
can divide a limited number of times
primary cell lines
tumour cell lines
can preform unlimited divisions
can preform unlimited divisions
tumour cell lines
what does plating out a liquid microbial culture onto solid media allow for
the number of colony forming units to be counted and tue density of cells in the culture to be estimated
what allows for number of colony forming units to be counted and tue density of cells in the culture to be estimated
plating out a liquid microbial culture on solid media
what is often needed when counting cells
serial dilution
what does serial dilution allow for
a suitable colony count
what is a haemocytometer used for
to estimate the cell numbers in a liquid culture
what is used to estimate the cell numbers in a liquid culture
haemocytometer
what does total cell count count
living and dead cells
what is required to identify and count viable cells
vital staining
function of vital staining
to identify and count viable cells
viable meaning
living
how does vital staining work
functional cell membranes prevent dyes getting through so only dead cells become coloured
viable cell count meaning
number of living cells
genome
total genetic material in a cell
total genetic material in a cell
genome
peoteome
entire series of proteins expressed by a genome
entire series of proteins expressed by a genome
proteome
why is the proteome greater than the genome
more than one protein can be produced from a single gene due to alternative RNA splicing
the _________ is larger than the _________ due to alternative RNA splicing
proteome, genome
in what organism is the the proteome larger than the genome
eukaryotes
non coding RNA genes
genes that do not code for proteins
genes that do not code for proteins
non coding RNA genes
what happens to non coding RNA genes
they are transcribed to produce..
* tRNA
* rRNA
* RNA molecules that control the expression of other genes
what are transcribed to produce..
* tRNA
* rRNA
* RNA molecules that control the expression of other genes
non coding RNA genes
factors affecting protein expression
- metabolic activity of the cell
- cellular stress
- response to signalling molecules
- diseased vs healthy cells
- metabolic activity of the cell
- cellular stress
- response to signalling molecules
- diseased vs healthy cells
factors affecting protein expression
what do eukaryotic cells have which increase the total area of the membrane
system of internal membranes
what does a system of internal membranes do
increase the total area of the membrane
what cells have a system of internal membranes
eukaryotic
eukaryotes surface area to volume ratio
relatively small surface area to volume ratio
why do eukaryotes have a small surface area to volume ratio
due to their size
problem with plasma membrane of eukaryotic cells
too small an area to carry out all the vital functions carried out by membranes
endoplasmic reticulum
forms a network of membrane tubules continuous with the nuclear membrane
forms a network of membrane tubules continuous with the nuclear membrane
endoplasmic reticulum
golgi apparatus
series of flattened membrane discs. proteins from the ER are packaged and processed here
series of flattened membrane discs. proteins from the ER are packaged and processed here
golgi apparatus
lysosomes
membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
lysosomes
vesicles
transport materials between membrane compartments
transport materials between membrane compartments
vesicles
what are membranes made up of
lipids and proteins
where are lipids and proteins synthesised
endoplasmic reticulum
rough endoplasmic reticulum ribosomes
has ribosomes on its cytosolic face
has ribosomes on its cytosolic face
RER
smooth endoplasmic reticulum ribosomes
lacks ribosomes
ER that lacks ribosomes
SER
where are lipids synthesised
the SER, and then inserted into its membrane
where does the synthesis of all proteins begin
in cytosolic ribosomes
whats synthesis begins in the cytosolic ribosomes
all proteins
where are cytosolic ribosomes
in the cytoplasm, not attached to the ER
synthesis of cytosolic proteins (3)
- begins in cytosolic ribosomes
- is completed in the cytosolic ribosomes
- the proteins remain in the cytosol
- begins in cytosolic ribosomes
- is completed in the cytosolic ribosomes
- the proteins remain in the cytosol
synthesis of cytosolic proteins
cytosol
liquid part of the cytoplasm
liquid part of the cytoplasm
cytosol
synthesis of transmembrane proteins (5)
- begins at the cytosolic ribosomes
- transmembrane proteins carry a signal sequence which halts translation
- this signal directs the ribosome synthesising the protein to dock with the ER to form the RER
- translation continues after docking and the protein is inserted into the membrane of the ER
- once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the golgi apparatus
- begins at the cytosolic ribosomes
- transmembrane proteins carry a signal sequence which halts translation
- this signal directs the ribosome synthesising the protein to dock with the ER to form the RER
- translation continues after docking and the protein is inserted into the membrane of the ER
- once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the golgi apparatus
synthesis of transmembrane proteins
how do proteins move around
move through golgi discs in vesicles that bud off from one disc to fuse with the next in the stack
signal sequence
short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell
short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell
signal sequence
enzymes in proteins becoming carbohydrates
enzymes catalyse the addition of various sugars in multiple steps to form carbohydrates
what happens to proteins as they move through the golgi
post translational modifications
when do proteins undergo post translational modifications
when they move through the golgi
major modification
addition of carbohydrate groups
addition of carbohydrate groups
major modification
vesicles that leave the golgi…
take proteins to the plasma membrane and lysosomes
movement of vesicles
they move along microtubules to other membranes and fuse with them within the cell
they move along microtubules to other membranes and fuse with them within the cell
vesicles
examples of secreted proteins
peptide hormones and digestive enzymes
peptide hormones and digestive enzymes
secreted proteins
what happens to secreted proteins in the secretory pathway (4)
- translated in ribosomes on the RER and enter its lumen
- the proteins move through the golgi apparatus and are then packaged into secretory vesicles
- these vesicles move to and fuse with the plasma membrane, releasing the protein out of the cell
- many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce proteins
- translated in ribosomes on the RER and enter its lumen
- the proteins move through the golgi apparatus and are then packaged into secretory vesicles
- these vesicles move to and fuse with the plasma membrane, releasing the protein out of the cell
- many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce proteins
secretory proteins in the secretory pathway
what is proteolytic cleavage
a form of post translational modification
example of protein that requires proteolytic cleavage
digestive enzymes
proteins are monomers/polymers
polymers
amino acid sequence determines what
protein structure
what are amino acids linked by
peptide bonds
what are linked by peptide bonds
amino acids
peptide bond
CONH
what is an amino acid made up of
- two functional groups:
amine (NH2)
carboxyl (COOH)
- variable region called an R group
- two functional groups:
amine (NH2)
carboxyl (COOH)
- variable region called an R group
amino acid
basic R groups
amine group (NH2)
amine group (NH2) property
basic
acidic R group
carboxyl (COOH)
carboxyl (COOH) property
acidic
polar R group
carbonyl (CO)
hydroxyl (OH)
amine (NH)
property of:
carbonyl (CO)
hydroxyl (OH)
amine (NH)
polar
hydrophobic R group
hydrocarbon group (CH3)
hydrocarbon group (CH3) property
hydrophobic
basic R groups are positively/negatively charged
positive
acidic R groups are positively/negatively charged
negatively
4 structures of protein
primary structure
secondary structure
tertiary structure
quaternary structure
primary structure
secondary structure
tertiary structure
quaternary structure
four structures of a protein
primary structure
sequence in which amino acids are synthesised into the polypeptide
sequence in which amino acids are synthesised into the polypeptide
primary structure
secondary structure of proteins
hydrogen bonding along the backbone of the protein results in regions of secondary structure
(alpha helices, parallel or anti parallel beta-pleated sheets, or turns)
hydrogen bonding along the backbone of the protein results in regions of secondary structure
(alpha helices, parallel or anti parallel beta-pleated sheets, or turns)
secondary structure of proteins
tertiary structure of proteins
polypeptide folds into a tertiary structure
this conformation is stabilised by interactions between R groups
polypeptide folds into a tertiary structure
this conformation is stabilised by interactions between R groups
tertiary structure of proteins
R group interactions
- hydrophobic interactions
- ionic bonds
- LDFs
- hydrogen bonds
- disulfide bridge
- hydrophobic interactions
- ionic bonds
- LDFs
- hydrogen bonds
- disulfide bridge
R group interactions
quaternary structure of proteins
this exists in proteins with two or more connected polypeptide subunits. it describes the spatial arrangement of the subunits
this exists in proteins with two or more connected polypeptide subunits. it describes the spatial arrangement of the subunits
quaternary structure
effect of increasing temperature on R group interactions
disrupts the interactions that hold the protein in shape
the protein begins to unfold and eventually becomes denatured
disrupts the interactions that hold the protein in shape
the protein begins to unfold and eventually becomes denatured
effect of increasing temperature on R group interactions
effect of changing pH on R group interactions
the charges of acidic and basic R groups are affected by pH
as pH increases or decreases from optimum, the normal ionic interactions between charged groups are lost
this gradually changes the conformation of the protein until it becomes denatured
the charges of acidic and basic R groups are affected by pH
as pH increases or decreases from optimum, the normal ionic interactions between charged groups are lost
this gradually changes the conformation of the protein until it becomes denatured
effect of pH on R group interactions
ligand
a substance that binds to a protein
a substance that binds to a protein
ligand
R groups and ligands
R groups not involved in protein folding can allow binding to ligands
what can ligands bind to on proteins
R groups not involved in protein folding
ligand binding sites on proteins
binding sites have complementary shape and chemistry to the ligand
what happens when a ligand binds to a protein binding site
conformation of the protein changes which causes a functional change in the protein
binding of what causes the conformation of the protein to change which causes a functional change in the protein
ligand
what do allosteric interactions occur between
spatially distinct sites of proteins
what occurs between spatially distinct sites of proteins
allosteric interactions
what do many allosteric proteins consist of
multiple subunits (quaternary structure)
what happens when a substance molecule binds to one site of an allosteric enzyme
increases the affinity of the other active sites for binding if subsequent substrate molecules
what increases the affinity of the other active sites for binding if subsequent substrate molecules
the binding of a substrate molecule to one active site of an allosteric enzyme
allosteric proteins with multiple subunits show what
cooperativity in binding
changes in binding at one subunit alters the affinity of the remaining subunits
what proteins show cooperativity in binding
allosteric proteins
allosteric enzymes have what
allosteric site
what do modulators regulate
the activity of the enzyme
what do modulators bind to
allosteric site of allosteric enzyme
what regulate the activity of enzymes by binding to the allosteric site
modulators
what do positive modulators do
increase the enzymes affinity for the substrate
what modulators increase the enzymes affinity for the substrate
positive modulators
what do negative modulators do
decreases the enzymes affinity for the substrate
what modulators decreases the enzymes affinity for the substrate
negative modulators
haemoglobin case study for allosteric enzyme
the binding and release of of oxygen at one subunit alters the affinity of the remaining subunits for oxygen
oxygen dissociation curve
at low temperatures concentrations at subunits on haemoglobin are tight together and it is difficult for oxygen to be absorbed
once one oxygen molecule binds, the structure of haemoglobin relaxed and it is easier to bind to the other subunits
effect of decrease in pH on haemoglobin
lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced
effect of increase in temperature on haemoglobin
lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced
what lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced
decrease in pH or increase in temperature
what can cause reversible conformational changes in proteins
addition or removal of phosphate
what does the addition or removal of phosphate to a protein
reversible conformational changes in proteins
what is the addition or removal of phosphate from a protein
a common post translational modification
how to make a protein from inactive to active
add phosphate group
how to make a protein from active to inactive
remove phosphate
what did kinase enzymes do
catalyse the transfer of a phosphate group to other proteins
the terminal phosphate of ATP is transferred to specific R groups in the protein
inactive -> active
what enzyme catalyses the transfer of a phosphate group to other proteins
the terminal phosphate of ATP is transferred to specific R groups in the protein
kinase
what do phosphatase enzymes do
catalyse the removal of a phosphate from a protein and add it to ADP, producing ATP
active -> inactive
what enzyme catalyses the removal of a phosphate from a protein and add it to ADP, producing ATP
active -> inactive
phosphatase
phosphorylation affect on protein
brings about conformational changes which can affect the activity of a protein
retina
area within the eye that detects light and contains two types of photoreceptor cells, rod cells and cone cells
area within the eye that detects light and contains two types of photoreceptor cells, rod cells and cone cells
retina
rod cells
functions in dim light but does not allow colour perception
functions in dim light but does not allow colour perception
rod cells
cone cells
responsible for colour vision and only function in bright light
responsible for colour vision and only function in bright light
cone cells
retinal and opsin combine to form what..
the photoreceptors of the eye, rhodopsin
retinal
light sensitive molecule
light sensitive molecule
retinal
opsin
membrane protein
membrane protein in the eye
opsin
retinal-opsin complex name in rod cells
rhodopsin
in what cells is the retinal-opsin complex called rhodopsin
rod cells
what does retinal do
absorbs a photon of light
what happens when retinal absorbs a photon of light
rhodopsin changes conformation to photoexcited rhodopsin
what happens when rhodopsin changes conformation to photoexcited rhodopsin
a cascade of proteins amplifies the signal
what happens when rhodopsin changes conformation to photoexcited rhodopsin
a cascade of proteins amplifies the signal
what happens when photoexcited rhodopsin activates a cascade
photoexcited rhodopsin activates a G protein called transducon which activates the enzyme phosphodiesterase (PDE)
what happens when retinal absorbs a photon of light (5)
- rhodopsin changes conformation to photoexcited rhodopsin. a cascade of proteins amplifies the signal
- rhodopsin rhodopsin activates a G protein called transducon which activates the enzyme phosphodiesterase (PDE)
- a single photoexcited molecule activates hundreds of molecules of G protein. each activated G protein activates one molecule of PDE. PDE catalyses the hydrolysis of a molecule called cyclic GMP (cGMP)
- each active PDE molecule breaks down thousands of cGMP per second. the reduction in cGMP concentration (as a result of its hydrolysis) affects the function of ion channels in the membrane of rod cells
- this results in the closure of ion channels in the membrane of the rod cells, which triggers nerve impulse in neurons in the retina
in rod cells, a high degree of amplification results in what
rod cells being able to respond to low intensities of light
what means rod cells are able to respond to low intensities of light
a very high degree of amplification
different photoreceptor proteins in cone cells
different forms of opsin combine with retinal to give different photoreceptor proteins, each with a maximal sensitivity to specific wavelengths : red, green, blue, or UV
cytoskeleton function
gives mechanical support and shape to cells
where do microtubules come from t
they radiate from the microtubule organising centre (MTOC) / centrosome
what radiate from the microtubule organising centre (MTOC) / centrosome
microtubules
what do microtubules form in cell division
spindle fibres
cytoskeleton must to what for cell division
remodel
the formation and breakdown of microtubules involves what
the polymerisation and depolarisation of tubulin
what involves the polymerisation and depolarisation of tubulin
the formation and breakdown of microtubules
what does the cell cycle consist of
- interphase
- mitotic (M) phase
what consists of..
- interphase
- mitotic (M) phase
cell cycle
interphase
involves growth and DNA synthesis including:
- G1 (growth)
- S (DNA replication)
- G2 (further growth)
mitotic (M) phase
involves the process of mitosis and cytokinesis
mitotic (M) phase
involves the process of mitosis and cytokinesis
involves the process of mitosis and cytokinesis
mitotic (M) phase
mitosis definition
the chromosomal material is separated by spindle microtubules
the chromosomal material is separated by spindle microtubules
mitosis
cytokinesis
the cytoplasm is separated into two daughter cells
the cytoplasm is separated into two daughter cells
cytokinesis
mitosis acronym
PMAT
prophase
DNA condenses into chromosomes, each consisting of two sister chromatids
nuclear membrane breaks down
DNA condenses into chromosomes, each consisting of two sister chromatids
nuclear membrane breaks down
prophase
microtubules in prophase
spindle microtubules extend from the MTOC by polymerisation and attach to chromosomes via their kinetochores in the centromere region
spindle microtubules extend from the MTOC by polymerisation and attach to chromosomes via their kinetochores in the centromere region
prophase
metaphase
chromosomes are aligned at the metaphase plate (equator of the spindle)
chromosomes are aligned at the metaphase plate (equator of the spindle)
metaphase
anaphase
spindle microtubules shorten by depolymerisation
sister chromatids are separated and chromosomes are pulled to opposite poles
spindle microtubules shorten by depolymerisation
sister chromatids are separated and chromosomes are pulled to opposite poles
anaphase
telophase
chromosomes decondense and nuclear membrane forms around each set of chromosomes
chromosomes decondense and nuclear membrane forms around each set of chromosomes
telophase
Polymerisation of tubulin causes…
Microtubules to grow
what causes microtubules to grow
Polymerisation of tubulin
Depolymerisation of tubulin causes…
Shrinkage of microtubules
What causes the shrinkage of microtubules
Depolymerisation of tubulin
G1
Growth phase
Growth phase
G1
S phase
DNA is replicated
Phase when DNA is replicated
S
G2 phase
Further growth phase
Further growth phase
G2
Checkpoints in cell cycle
G0, G1, G2, and metaphase
G0, G1, G2, and metaphase
Checkpoints in cell cycle
Checkpoints definition
Mechanisms within the cell that assess its condition during the cell cycle and hand progression to the next phase unless certain requirements are met
Mechanisms within the cell that assess its condition during the cell cycle and hand progression to the next phase unless certain requirements are met Mechanisms within the cell that assess its condition during the cell cycle and hand progression to the next phase unless certain requirements are met
Checkpoints
G0 phase
- Resting phase
- some cells go here temporarily (lack of resources)
- some cells are always in this phase and don’t divide
- Resting phase
- some cells go here temporarily (lack of resources)
- some cells are always in this phase and don’t divide
G0 phase
Why would cells enter the G0 phase
If not enough cyclin is produced
What happens if not enough cyclin is produced
Cells may enter the G0 phase
G1 checkpoint
- occurs towards the end of G1 and the size of the cell is checked to confirm that there is sufficient cell mass for daughter cells to be produced
- dna damage monitored and damage can trigger the activation of several proteins, including p53
- cyclin proteins that accumulate during cell growth are involved in regulating the cell cycle
- cyclins combine with and activate cyclin-dependent kinases (CDK’s). Active cyclin-CDK complexes phosphorylate proteins that regulate the progression through the cell cycle. If sufficient phosphorylation is reached, progression occurs
- retinoblastoma protein (Rb) acts as a tumour suppressor by inhibiting the transcription of genes that code for proteins needed for DNA replication
- cells don’t enter the S phase if Rb is unphosphorylated, so they don’t undergo DNA replication. They can’t progress to the M phase to undergo cell division. Thus, Rb acts as a tumour suppressor
- Cyclins build up and phosphorylation by cyclin-CDK inhibits Rb, which allows transcription of the genes that code for proteins needed for DNA replication. Cells progress from G1 to S phase where replication occurs
- occurs towards the end of G1 and the size of the cell is checked to confirm that there is sufficient cell mass for daughter cells to be produced
- dna damage monitored and damage can trigger the activation of several proteins, including p53
- cyclin proteins that accumulate during cell growth are involved in regulating the cell cycle
- cyclins combine with and activate cyclin-dependent kinases (CDK’s). Active cyclin-CDK complexes phosphorylated proteins that regulate the progression through the cell cycle. If sufficient phosphorylation is reached, progression occurs
- retinoblastoma protein (Rb) acts as a tumour suppressor by inhibiting the transcription of genes that code for proteins needed for DNA replication
- cells don’t enter the S phase if Rb is unphosphorylated, so they don’t undergo DNA replication. They can’t progress to the M phase to undergo cell division. Thus, Rb acts as a tumour suppressor
Cyclins build up and phosphorylation by G1 cyclin-CDK inhibits the Rb protein, which allows transcription of the genes that code for proteins needed for DNA replication. Cells progress from G1 to S phase where replication occurs
G1 checkpoint
p53 function
Can stimulate DNA repair, arrest the cell cycle, or cause cell death
Can stimulate DNA repair, arrest the cell cycle, or cause cell death
p53
G2 checkpoint
- The success of DNA replication and any damage to DNA is assessed
- From here, cells progress into the M phase, where mitosis occurs
- The success of DNA replication and any damage to DNA is assessed
- From here, cells progress into the M phase, where mitosis occurs
G2 checkpoint
Metaphase checkpoint
- a metaphase checkpoint controls progression from metaphase to anaphase
- at the checkpoint, progression is halted until the chromosomes are aligned correctly on the metaphase plate and attached to the spindle microtubules
- this checkpoint controls entry to anaphase
- a metaphase checkpoint controls progression from metaphase to anaphase
- at the checkpoint, progression is halted until the chromosomes are aligned correctly on the metaphase plate and attached to the spindle microtubules
- this checkpoint controls entry to anaphase
Metaphase checkpoint
What does an uncontrolled increase increase in the rate of cell cycle cause
May result in tumour formation
Proto-oncogene as example of tumour
Proto-oncogene is a normal gene, usually involved in the control of cell growth or division, that can mutate not form a tumour-promoting oncogene
What can cause a degenerative disease
An uncontrolled reduction in the rate of cell cycle
What does an uncontrolled reduction in the rate of cell cycle cause
Degenerative disease
Alternation in the normal control of cell cycle is thought to lead to what
Expression of certain proteins associated with Alzheimer’s disease, eventually resulting in neuronal cell death
Apoptosis
Programmed cell death, which can occur during normal growth and development, resulting in the removal of old or damaged cells or during metamorphosis in certain species
Programmed cell death, which can occur during normal growth and development, resulting in the removal of old or damaged cells or during metamorphosis in certain species
Apoptosis
What can apoptosis be used for
Killing cells that have started to divide in an uncontrolled way during tumour formation
What is apoptosis triggered by
Cell death signals, which can be external or internal
What can cell death signals be
- external
- internal
External cell death signals
The production of death signal molecules from lymphocytes
External death signal molecules bind to surface receptor protein and trigger a protein cascade within the cytoplasm
The production of death signal molecules from lymphocytes
External death signal molecules bind to surface receptor protein and trigger a protein cascade within the cytoplasm
External cell death signals
Internal cell death signals
DNA damage is an example of internal death signal or lack of cell growth factors
An internal death signal resulting from DNA damage causes activation of p53 rumour-suppressor protein
DNA damage is an example of internal death signal or lack of cell growth factors
An internal death signal resulting from DNA damage causes activation of p53 rumour-suppressor protein
Internal death cell signals
What do death signals result from
The activation of protease enzymes called caspases, which act in cascades to cause the destruction of the cell
What happens when there is activation of protease enzymes - caspases, which act in cascades to cause the destruction of the cell
Death signals
When might cells initiate apoptosis
In absence of growth factors
What would cells do in absence of growth factors
Initiate apoptosis
Extracellular space is hydrophilic/hydrophobic
Hydrophilic
Polarity of inside the membrane
Nonpolar
Polarity of membrane surface
Polar
What do all types of death signals results in
The activation of caspases (type of protease enzyme) that cause the destruction of the cell
