U1 -KA2 - PROTEINS - 1)proteins + synthesis of lipids and proteins Flashcards
What is the proteome
The proteome is the entire set of proteins expressed by a genome
What is a genome
An organisms genome is its complete set of DNA including both the protein coding genes and the non coding RNA genes
What do non coding RNA genes include.
Those that are transcribed to produce tRNA , rRNA and RNA molecules that control expression of other genes
Why is the proteome larger than the number of genes
The proteome is larger than the number of genes , particularly in eukaryotes , due to alternative RNA splicing - because more than one proteins can be expressed from a single gene.
One gene may code for many proteins (one gene can produce several different mature mRNA transcripts and therefore proteins.
What is alternative RNA splicing
RNA splicing: When mRNA is transcribed into eukaryotic cells it is composed of introns (non-coding sequence, not expressed in proteins) these are spliced out of the mRNA. Exons - coding sequences, which will be expressed in the protein molecule. Depending on which RNA segments are treated as exons and introns in a primary RNA transcript of a gene , different nature mRNA molecules are produced
One ____ may code for many ______
- this would result in different sequences of _____ ______ / R groups
- so result in different folding / conformation creating different proteins
One gene may code for many proteins (one gene can produce several different mature mRNA transcripts and therefore proteins)
- this would result in different sequences of amino acids / R groups
- so result in different folding / conformation creating different proteins
- How many genes is human genome
- How many proteins is human proteome
Human genome - around 30,000 genes
Human proteome - over 100,000 proteins
Not all _____ are expressed as ______ in a particular cell
Not all genes are expressed as proteins in a particular cell
.. and so: the set of proteins expressed by a given cell type can vary over time and under different conditions. Some factors effecting the set of proteins expressed by a given cell type :
- metabolic activity of the cell
- it’s state of cellular stress depending on extremes of temperature , pH exposure to toxins , mechanical damage etc
- it’s response to signalling molecules such as hormones and in the case of lymphocytes the antigens to which it is exposed
- it’s state of health or disease and / or during apoptosis
Prokaryotic cells (____) are much smaller than cells of eukaryotes (_____). why?
Prokaryotes (bacteria and archaea) are much smaller than cells of eukaryotes (fungi, plant and animals). The key structural difference that explains this is NOT the presence or absence of a nucleus but the presence or absence of intracellular membrane structures.
Do prokaryotic cells have intercellular membrane structures ?
Where are most of their functions carried out then?
How does this relate to their size?
- These cells do not have intracellular membrane structures in their cytoplasm.
- many functions of these structures are carried out by the plasma membrane , so this places a limit on the maximum rate of metabolic processes in the prokaryotic cells.
- this metabolic limit in turn restricts the maximum size that prokaryotic cells can attain.
What does the size difference mean between eukaryotic cells and prokaryotic cells, (SA :V ratio )
- the size difference means eukaryotes have a relatively small surface area to volume ratio.
- even the smaller eukaryote has 8x the volume of largest prokaryote, but the plasma membrane is only four times larger
What does it mean that a eukaryote has a small SA:V ratio, what does the cell have?
This means that the plasma membrane of the eukaryote has too small an area to carry out all the vital functions carried out by membranes.
- the total rate of all these processes would be too slow to provide materials to support the cell
How is the increase in size in a eukaryotes supported ?
This increase in size can only be supported because the eukaryotes have a system of internal membranes called the endoplasmic reticulum which increases the total area of membrane available for the vital metabolic processes
Endoplasmic reticulum explained
- to increase the total area of membrane area , eukaryotic cells have a system of internal membranes :called the endoplasmic reticulum (ER) which forms a network of membrane tubules , continuous with the nuclear membrane
Describe how vesicles are able to move around the cell
-vesicles transport materials between membrane compartments or to the plasma membrane Along microtubules (to other membranes )
Types of ER : Rough / smooth and their properties
The ER is either rough (RER) or smooth (SER)
- RER has docked ribosomes on its cystolic face
- SER lacks ribosomes
What is the Golgi apparatus
A series of flattened membrane discs and has associated vesicles that transport materials between membrane compartments
- and also it is where proteins undergo post translational modification
What are lysosomes / how are they formed
- lysosomes are membrane bound organelles , containing a variety of hydrolyse enzymes that can digest proteins , lipids, nucleic acids and carbohydrates
- they form from specialised Golgi vesicles
- the inside of lysosomes are acidic allowing optimal function of the enzymes it contains
What are the two parts of the cytoplasm
- first part is the cytosol which is the liquid component of the cytoplasm
- the second party is the ribosomes and the membrane bound organelles (such as ,ER ,Golgi apparatus,mitochondria+ chloroplast) which are suspended in the cystol
How and where is the synthesis of cytosolic proteins done
- what proteins do these include
- the synthesis of cytosolic proteins is done entirely by cytosolic ribosomes, once completed they are released into the cytosol (and remain in the cytosol )
- these proteins include the enzymes of glycolysis + enzymes that attach amino acids to tRNA molecules for use in protein synthesis in the ribosome.
Recap cell membrane : what are they composed of
- phospholipid and proteins are the main membrane components. - phospholipid molecules have a hydrophilic head and hydrophobic tails and form into a bi layer.
How is the synthesis of lipids carried out
Synthesis of lipids (oils, phospholipids + steroid hormones) is carried out in the SER (by enzymes embedded in membrane of SER) and then they are inserted into the membrane of SER
Remember: smooth ER has NO ribosomes attached
Where does the synthesis of ALL proteins START
The synthesis of all proteins begins in cytosol of ribosomes
- remember the synthesis of cytosolic proteins is completed there and they remain in the cystol to carry out specific functions
How / where is the synthesis of transmembrane proteins done
- synthesis of transmembrane proteins starts in the cytosolic ribosomes ( as all proteins) but is completed elsewhere - when the relevant cystolic ribosomes dock with the ER to become part of the RER
Transmembrane proteins are ________ to the membrane and permanently ________ there.
Transmembrane proteins are intregal to the membrane and are permanently attached there
Not all integral proteins are _____________ .
Not all internal proteins are transmembrane
Peripheral proteins are not ________ , they from weak bonds on the surface of the membrane , either with the phospholipid heads or exposed parts of intregal proteins
Peripheral proteins are not embedded , they from weak bonds on the surface of the membrane , either with the phospholipid heads or exposed parts of intregal proteins
Steps for the synthesis of transmembrane proteins
- transmembrane proteins carry a signal sequence , a short stretch of 16-30 amino acids at one end of the polypeptide which will determine the eventual location of that protein in a cell
- a polypeptide that will become part of a transmembrane protein will start off as a short stretch of around 20 amino acids- signal sequence
- when a signal sequence emerges from the ribosome a cytosolic particle binds to it and this temporarily halts translation
- the particle also directs the ribosome to dock with a protein pore in the ER thus forming the RER
- after docking the protein pore removes the cytosolic particle and signal sequence so translation continues
- as it’s translated , the polypeptide chain is inserted directly in the membrane of the ER. The ribosome is released back into the cystol once translation is completed
Synthesis of other proteins : proteins destined for use in the mitochondria , chloroplast or the interior of the nucleus
-proteins that are destined for use in the mitochondria, chloroplasts, or the interior of the nucleus are synthesised entirely by cystolic ribosomes. After the protein has been released from the ribosome into the cytosol , these proteins have other signal sequence which are used to direct them to their correct organelle
Synthesis of other proteins : polypeptides that are destined to be part of a lysosome enzyme or part of a secreted protein
- polypeptides that are destined to be part of a lysosome enzyme or part of a secreted protein start their synthesis at a cystolic ribosome and, like the transmembrane proteins , have a signal sequence that takes the ribosome to the RER.
- however , as they are translated through the protein pore in the RER, they are released directly into the lumen of the RER instead of being inserted into the membrane
As proteins go through the Golgi apparatus they undergo ____ - _____________-____________
As proteins go through the Golgi apparatus , they undergo pos translational modification
Reminder: what is the Golgi apparatus
Stack of hollow and flattened membrane discs
Explain post translational modification in the Golgi apparatus ( the entering and what happens)
- the polypeptides that are produced in the RER are transported by vesicles (vesicles that bud off from the RER)
- the vesicles move along microtubules and then fuse with the Golgi apparatus
- the polypeptides move through the stack of Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack
- as polypeptides move through the stack of discs they undergo PTM
- the addition of carbohydrate is the major modification involved
- enzymes catalyse the addition of various sugars in multiple steps to form carbohydrates groups attached to the polypeptide, modifying it , this results in glycoproteins
Most ________ proteins are glycoproteins
Most secreted proteins are glycoproteins.
- they are also found in the membrane where they are important for “self” recognition by the immune system
Leaving the Golgi apparatus (explain final steps and how protein leaves the Golgi apparatus)
- before a protein leaves the Golgi apparatus, phosphate groups can be added to identify its final destination.
- vesicles carrying the protein bud off and leave the Golgi apparatus
These vesicles move along microtubules to other membranes and fuse with them. There are 4 possible fates of these vesicles
The 4 possible fates of the vesicles after leaving the Golgi apparatus
1) they can fuse with the plasma membrane to build the membrane and add transmembrane proteins
2) can fuse with plasma membrane to allow a protein to be secreted (secretory pathway)
3) can fuse with the membranes of mitochondria , chloroplasts or nucleus to build their outer membranes and add transmembrane proteins
4) the vesicle can form a lysosome in the cytosol
As proteins go through the Golgi apparatus they undergo post translational modification , what is the major modification involved
The addition of carbohydrate is the major modification involved
Examples of post translational modification
- addition of a carbohydrate
- proteolytic cleavage
- phosphorylation
Examples of secreted proteins
Peptide hormones (insulin) and digestive enzymes (such as trypsin) are examples of secreted proteins.
Explain the secretory pathway
- as described before the synthesis of the polypeptides of secreted proteins starts at the cystolic ribosomes and is completed after the ribosomes have docked with the RER.
- unlike polypeptides of transmembrane proteins , the polypeptide of the secretes protein enters the lumen of the RER
- the polypeptide undergoes PTM as they move through the discs of the Golgi apparatus and are then packaged into secretory vesicles
- these vesicles move along microtubules to fuse with the plasma membrane , so releasing the proteins out of the cell.
(Some may develop into lysosomes-retained within the cytosol)
What is proteolytic cleavage ?
- proteolytic cleavage is another type of post translational modification
- many proteins which are to be secreted are synthesised as inactive precursors and required proteolytic cleavage to produce active proteins
Examples of proteolytic cleavage
- a section of proinsulin chain is cut and removed to form active insulin - this is an example of proteolytic cleavage
- digestive enzyme pepsin is secretes then undergoes proteolytic cleavage by acid in the stomach before it becomes active
- insulin undergoes proteolytic cleavage in the secretory vesicles before being secreted
