U1 -KA2 - PROTEINS - 1)proteins + synthesis of lipids and proteins

Question 1

What is the proteome

Answer 1

The proteome is the entire set of proteins expressed by a genome

Question 2

What is a genome

Answer 2

An organisms genome is its complete set of DNA including both the protein coding genes and the non coding RNA genes

Question 3

What do non coding RNA genes include.

Answer 3

Those that are transcribed to produce tRNA , rRNA and RNA molecules that control expression of other genes

Question 4

Why is the proteome larger than the number of genes

Answer 4

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.

Question 5

What is alternative RNA splicing

Answer 5

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

Question 6

One ____ may code for many ______

• this would result in different sequences of _____ ______ / R groups
• so result in different folding / conformation creating different proteins

Answer 6

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

Question 7

• How many genes is human genome

- How many proteins is human proteome

Answer 7

Human genome - around 30,000 genes

Human proteome - over 100,000 proteins

Question 8

Not all _____ are expressed as ______ in a particular cell

Answer 8

Not all genes are expressed as proteins in a particular cell

Question 9

.. 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 :

Answer 9

• 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

Question 10

Prokaryotic cells (____) are much smaller than cells of eukaryotes (_____). why?

Answer 10

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.

Question 11

Do prokaryotic cells have intercellular membrane structures ?
Where are most of their functions carried out then?
How does this relate to their size?

Answer 11

• 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.

Question 12

What does the size difference mean between eukaryotic cells and prokaryotic cells, (SA :V ratio )

Answer 12

• 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

Question 13

What does it mean that a eukaryote has a small SA:V ratio, what does the cell have?

Answer 13

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

Question 14

How is the increase in size in a eukaryotes supported ?

Answer 14

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

Question 15

Endoplasmic reticulum explained

Answer 15

• 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

Question 16

Describe how vesicles are able to move around the cell

Answer 16

-vesicles transport materials between membrane compartments or to the plasma membrane
Along microtubules (to other membranes )

Question 17

Types of ER : Rough / smooth and their properties

Answer 17

The ER is either rough (RER) or smooth (SER)

• RER has docked ribosomes on its cystolic face
• SER lacks ribosomes

Question 18

What is the Golgi apparatus

Answer 18

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

Question 19

What are lysosomes / how are they formed

Answer 19

• 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

Question 20

What are the two parts of the cytoplasm

Answer 20

• 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

Question 21

How and where is the synthesis of cytosolic proteins done

- what proteins do these include

Answer 21

• 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.

Question 22

Recap cell membrane : what are they composed of

Answer 22

• phospholipid and proteins are the main membrane components. - phospholipid molecules have a hydrophilic head and hydrophobic tails and form into a bi layer.

Question 23

How is the synthesis of lipids carried out

Answer 23

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

Question 24

Where does the synthesis of ALL proteins START

Answer 24

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

Question 25

How / where is the synthesis of transmembrane proteins done

Answer 25

• 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

Question 26

Transmembrane proteins are ________ to the membrane and permanently ________ there.

Answer 26

Transmembrane proteins are intregal to the membrane and are permanently attached there

Question 27

Not all integral proteins are _____________ .

Answer 27

Not all internal proteins are transmembrane

Question 28

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

Answer 28

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

Question 29

Steps for the synthesis of transmembrane proteins

Answer 29

• 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

Question 30

Synthesis of other proteins : proteins destined for use in the mitochondria , chloroplast or the interior of the nucleus

Answer 30

-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

Question 31

Synthesis of other proteins : polypeptides that are destined to be part of a lysosome enzyme or part of a secreted protein

Answer 31

• 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

Question 32

As proteins go through the Golgi apparatus they undergo ____ - _____________-____________

Answer 32

As proteins go through the Golgi apparatus , they undergo pos translational modification

Question 33

Reminder: what is the Golgi apparatus

Answer 33

Stack of hollow and flattened membrane discs

Question 34

Explain post translational modification in the Golgi apparatus ( the entering and what happens)

Answer 34

• 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

Question 35

Most ________ proteins are glycoproteins

Answer 35

Most secreted proteins are glycoproteins.

- they are also found in the membrane where they are important for “self” recognition by the immune system

Question 36

Leaving the Golgi apparatus (explain final steps and how protein leaves the Golgi apparatus)

Answer 36

• 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

Question 37

The 4 possible fates of the vesicles after leaving the Golgi apparatus

Answer 37

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

Question 38

As proteins go through the Golgi apparatus they undergo post translational modification , what is the major modification involved

Answer 38

The addition of carbohydrate is the major modification involved

Question 39

Examples of post translational modification

Answer 39

• addition of a carbohydrate
• proteolytic cleavage
• phosphorylation

Question 40

Examples of secreted proteins

Answer 40

Peptide hormones (insulin) and digestive enzymes (such as trypsin) are examples of secreted proteins.

Question 41

Explain the secretory pathway

Answer 41

• 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)

Question 42

What is proteolytic cleavage ?

Answer 42

• 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

Question 43

Examples of proteolytic cleavage

Answer 43

• 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