Unit 1 Flashcards
Why is the proteome larger than the number of genes?
More than one protein can be produced from a single gene as a result of alternative RNA splicing
Where does post-translational modification take place?
Rough endoplasmic reticulum, Golgi apparatus and the target site of the protein
What can make the set of proteins expressed by a given cell type change?
Metabolic activity of the cell, cellular stress, the response to signalling molecules and diseased versus healthy cells.
Isoelectric point
The pH at which the protein has no net charge
Centrifugation separates substances in a liquid using their…
Density
TL Chromatography separates mixtures eg amino acids by using…
Solubility of the different components
Speed that each solute travels along the chromatogram depends on its differing solubility in the solvent used
Affinity chromatography separates proteins using…
A highly specific interaction eg between an antigen and antibody
Electrophoresis separates proteins and nucleic acids using…
Size (length/mass)
How does the SDS- PAGE technique differ from other gel electrophoresis?
It gives all molecules an equally negative charge and so separates by size alone
Name of protein markers on an antigen
Epitopes
Polyclonal antibodies v monoclonal antibodies
PC antibodies bind with more than one type of antigen where as MC antibodies bind with only one type of epitope on the antigen and so are highly specific.
Example of an immunoassay technique
ELISA
Example of hazards in a lab
Toxic or corrosive chemicals, heat or flammable substances, pathogenic organisms and mechanical equipment
Risk
The likelihood of harm arising from exposure to hazard
Linear dilution
Dilutions differ by an equal interval eg 0.1 0.2 0.3
Log dilution
Dilutions differ by a constant proportion eg.10-1 10-2 10-3
How does a centrifuge separate substances of differing density
More dense components settle in the pellet, less dense components remain in the supernatant
Describe affinity chromatography
A solid matrix or gel column is created with specific molecules bound to the matrix or gel. Soluble target proteins in a mixture with a high affinity for these molecules, become attached to them as the mixture passes down the column. Other non-target molecules with a weaker affinity are washed out.
How does gel electrophoresis work
Charged macromolecules move through an electric field applied to a gel matrix
How do native gels separate proteins
These gels do not denature the molecule so that separation is by size, shape and charge
What are immunoassay techniques used for
To detect and identify specific proteins
Describe western blotting
A technique used after SDS-PAGE electrophoresis
The separated proteins from the gel are transferred onto a solid medium
The proteins can be identified using specific antibodies that have reporter enzymes attached
Bright-field microscopy
Commonly used to observe whole organisms, parts of organisms, thin sections of dissected tissue or individual cells
Fluorescence microscopy
Uses specific fluorescent labels to bind to and visualise certain molecules or structures within cells or tissues
Describe Aseptic technique
Eliminates unwanted microbial contaminates when culturing micro organisms or cells
Involves the sterilisation of equipment and culture media by heat or chemical means
Growth factors
Proteins that promote cell growth and proliferation
Essential for the culture of most animal cells
Method of achieving a suitable colony count
Serial dilution
Method to estimate cells numbers in a liquid culture
Use of haemocytometer
Method for counting viable cells
Vital staining
Proteome
Entire set of proteins expressed by a genome
What are non-coding RNA genes used for?
Transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes
How does the system of internal membranes affect eukaryotes
Increases the total area of membrane
Eukaryote surface area to volume ratio
Small due to their size
This means the plasma membrane of a eukaryote is too small to carry out all the vital functions carried out by membranes
Describe the endoplasmic reticulum
Forms a network of membrane tubules continuous with the nuclear membrane
Describe the Golgi apparatus
It is a series of flattened membrane discs
What are lysosomes
Membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
Function of vesicles
Transports materials between membrane compartments
Where are lipids and proteins synthesised
Endoplasmic reticulum
Difference between rough ER and smooth ER
RER has ribosomes on its cytosolic face while SER lacks ribosomes
Synthesis of lipids
Synthesised in SER and inserted into its membrane
Where does the synthesis of all proteins begin
Cytosolic ribosomes
Synthesis of cytosolic proteins
Synthesised in cytosolic proteins and these proteins remain in the cytosol
Function of the signal sequence transmembrane proteins carry
Halts translation and directs the ribosome synthesising the protein to dock with the ER forming RER
Translation continues after docking and the protein is inserted into the membrane of the ER
Describe a signal sequence
A short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell
What happens once the proteins are in the ER
They are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus
Major modification in post translational modification
The addition of carbohydrate groups
Function of vesicles that leave the Golgi apparatus
Take proteins to the plasma membrane and lysosomes
Vesicles move along microtubules to other membranes and fuse with them within the cell
What happens as proteins move though the Golgi apparatus
They undergo post translational modification
Post translational modification
Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack. Enzymes catalyse the addition of various sugars in the multiple steps to form the carbohydrates.
example of secreted proteins
peptide hormones and digestive enzymes
where are secreted proteins translated
ribosomes on the RER and then enter its lumen
then where do translated secreted proteins go
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 proteins out of the cell
what are many secreted proteins synthesised as?
inactive precursors and require proteolytic cleavage to produce active proteins
what is proteolytic cleavage ?
another type of post translational modification
how do the R groups of amino acids differ
vary in size, shape, charge, h bonding capacity, chemical reactivity
four type of amino acids
basic, acidic, polar, hydrophobic
how do different proteins have different functions
function is dependant on R group
what is the primary structure
the sequence in which the amino acids are synthesised into the polypeptide
3 main types of secondary structure
alpha helices, parallel or anti-parallel beta-pleated sheets and turns
how does an alpha helix form?
twisting the polypeptide chain into a helix then stabilising with h bonds
what type of beta pleated sheet is the most stable
antiparallel is more stable as h bonding is more optimal
how is the conformation to tertiary structures stabilised ?
by interactions between R groups: hydrophobic interactions, ionic bonds, London dispersion forces and disulfide bridges
describe a quaternary structure
exists in proteins with two or more connected polypeptide subunits
it describes the spatial arrangement of subunits
what is a prosthetic group
a non-protein unit tightly bound to a protein and necessary for its function
what are disulfide bridges
covalent bonds between R groups containing sulfur
example of a prosthetic group
the ability of haemoglobin to bind oxygen is dependant upon the non-protein haem group
what influences interactions of the R groups
temperature and pH
how does temp impact interactions between R groups
Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured
how does pH impact interactions between R groups
The charges on acidic and basic R groups are affected by pH. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured
what is a ligand
a substance that can bind to a protein
describe ligand binding
R groups not involved in protein folding can allow binding to ligands
binding sites will have complementary shape and chemistry to the ligand
as a ligand binds to a protein binding site the conformation of the protein changes.
what happens after a ligand has bound to a protein
a change in conformation causes a functional change in the protein
where do allosteric interactions occur?
between spatially distinct sites
what causes the affinity of the other active sites for binding of subsequent substrate molecules to increase?
the binding of a substrate molecule to one active site of an allosteric enzyme
what kind of structure do allosteric proteins have
quaternary
consists of multiple subunits
how do allosteric proteins show co-operativity in binding
changes in binding at one subunit alter the affinity of the remaining subunits
what is the second type of site allosteric enzymes contain
allosteric site
role of a modulator
regulate the activity of the enzyme when they bind to the allosteric site
what happens after the binding of a modulator
the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
example of co-operativity
the binding and release of oxygen in haemoglobin
Changes in binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen
difference between positive and negative modulators
PM increase the enzymes affinity for the substrate whereas negative modulators reduce the enzymes affinity
how does pH and temp influence the binding of oxygen
A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue
the addition or removal of phosphate can cause …
reversible conformational change in proteins
common form of post translational modification
role of protein kinase
catalyse the transfer of a phosphate group to other proteins
describe binding of phosphate
the terminal phosphate of ATP is transferred to specific R groups
protein phosphates catalyse the reverse reaction
phosphorylation brings about conformational changes which can affect a proteins activity
the activity of many cellular proteins such as enzymes and receptors is regulated in this way
adding a phosphate groups adds…
negative charges
ionic interactions in the unphosphorylated protein can be disrupted and new ones created
describe peripheral proteins
they have hydrophilic R groups on their surface and are bound to the surface of membranes, mainly by ionic and hydrogen bond interactions
how are integral proteins held in the phospholipid bilayer
regions of hydrophobic R groups allow hydrophobic interactions to hold the proteins
what do integral membrane proteins interact with
interact extensively with the hydrophobic region of membrane phospholipids
what do peripheral membrane proteins interact with
the surfaces of integral membrane proteins
what can and cant pass through the phospholipid bilayer
ions and most uncharged polar molecules cannot
some small molecules such as oxygen and CO2 pass through the bilayer by simple diffusion
facilitated diffusion
is the passive transport of substances across the membrane through specific transmembrane proteins
describe channel proteins
Channels are multi-subunit proteins with the
subunits arranged to form water-filled pores
that extend across the membrane
most channel proteins in animal and plant cells are highly selective
what allows cells to perform specialised functions
different cell types have different channel and transporter proteins
how do some channel proteins allow or prevent diffusion
they are gated and change conformation to do this
what are ligand - gated channels controlled by
binding of signal molecules
what are voltage-gated channels controlled by
changes in ion concentration
describe how transporter proteins transport
they bind to the specific substance to be transported and undergo a conformational change to transfer the solute across the membrane
active transport
uses pump proteins that transfer substances across the membrane against their conc. gradient
a source of metabolic energy is required
describe the pumps that mediate active transport
transporter proteins coupled to an energy source
how do some proteins provide the energy for active transport and why
some active transport proteins hydrolyse ATP directly to provide the energy for the conformational change required to move substances across the membrane
what hydrolyses ATP
ATPases
what combines to form the electrochemical gradient for a solute carrying a net charge
the concentration gradient and the electrical potential difference
what does the electrochemical gradient determine
the transport of the solute
where does the SP pump get its energy from
ATP hydrolysis
describe active transport in a SP pump
The pump has high affinity for sodium ions inside the cell; binding occurs; phosphorylation by ATP; conformation changes; affinity for sodium ions decreases; sodium ions released outside of the cell; potassium ions bind outside the cell; dephosphorylation; conformation changes; potassium ions taken into cell; affinity returns to start
describe how ATP hydrolysis affects the SP pump
For each ATP hydrolysed, three sodium ions are transported out of the cell and two potassium ions are transported into the cell. This establishes both concentration gradients and an electrical gradient
example of SP pump in humans
In the small intestine, the sodium gradient created by the sodium-potassium pump drives the active transport of glucose
SP pump is in intestinal epithelial cells
glucose support in small intestine
The glucose transporter responsible for this glucose symport transports sodium ions and glucose at the same time and in the same direction
