1.2 Proteins Flashcards
Define the Genome
The genome is the complete set of DNA in an organism
Define the Proteome
The proteome is the entire set of proteins that can be expressed from the organisms genome
Why is the Proteome larger than the Genome?
Due to alternative RNA splicing, more that one protein can be produced from a single gene.
What are genes that do not code for proteins called?
Non-coding RNA genes
Non-coding RNA genes include…
Those that are transcribes to produce tRNA, rRNA and RNA molecules that control the expression of other genes.
What are the factors that can affect the set of proteins expressed by a given cell type?
- Metabolic activity of the cell
- Cellular stress
- The response to signalling molecules
- diseased vs healthy cells
A structural feature of Eukaryotic cells is that….
And this means…..
They have a relatively small surface area to volume ratio
And this means the plasma membrane of eukaryotic cells is too small an area to carry out all the vital functions carried out by a membrane.
What feature do eukaryotic cells have that overcomes the problem of a small plasma membrane and how do they do it?
They have a system of internal membranes (Endomembranes)
They increase the total surface area of membrane within the cell
State 4 organelles of the endomembrane
- Endoplasmic Reticulum (ER)
- Golgi Apparatus
- Lycosomes
- Vesicles
Describe the Endoplasmic Reticulum (ER)
The ER is a membrane system which forms a network of membrane tubles. It is continous with the nuclear membrane
Describe the Golgi Apparatus
A series of flattened membrane disks
Describe Lysosomes
Lysosomes are membrane boung organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
Describe Vesicles
Vesicles transport materials between membrane compartments
Where in a cell are lipids and proteins synthesised
Endoplasmic Reticulum
Describe the types of Endoplasmic Reticulum
Smooth ER - Lacks ribosomes
Rough ER - Has ribosomes on its cystolic face
Where are the lipids formed and how do they get to their position
In the Smooth ER and then inserted into the membrane
Where does the synthesis of proteins begin
Cystolic ribosomes
Describe how transmembrane proteins move from cystolic ribosomes to the ER
Transmembrane proteins carry a signal sequence, which halts translation and gets the ribosome synthesising the protein to dock with the endoplasmic reticulum forming RER.
Translation continues after docking and the protein is inserted into the membrane of the ER
What is a signal sequence
A signal sequence is 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 to proteins once they enter the ER
They are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.
What happens to proteins as they travel through the Golgi Apparatus
They undergo post-translational modification
What is Post-translational modification
Changing the properties of a protein by proteolytic cleavage and adding a modifying group, such as acetyl to one or more amino acids
What Post-translational modification typically occurs in the Golgi apparatus
The addition of carbohydrate groups
How do proteins move through the Golgi apparatus
Protein molecules move through the Golgi discs in vesicles which bud off from one disc and fuse to the next one in the stack.
What is the role of Enzymes in the movement of proteins in the Golgi apparatus
Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates.
What happens when vesicles leave the golgi apparatus
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.
Whats an example of a secreted protein?
Peptide hormones and digestive enzymes
Where are secreted proteins translated
In Ribosomes on the RER
Describe the pathway of a secreted protein from its exit from the RER to its release outside the cell
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 outside of the cell.
What state are many secreted proteins synthesised as
inactive
What process is used to activate inactive secreted proteins
Proteolytic cleavage
What is Proteolytic cleavage
Another type of post-translational modification.
The removal of a section of sequence.
Whats one example of inactive secreted proteins that undergo Proteolytic cleavage
Digestive enzymes
Proteins are made up of
Amino acid monomers
How are amino acids linked together
By peptide bonds to form polypeptides
Whats is the formula of a peptide bond
O H
|| |
C —N
What are the differences and similarities between different amino acids
The same basic structure
Different R-Groups
R groups of amino acids can vary in..
- Size
- Shape
- Charge
- Hydrogen bonding capacity
- Chemical reactivity
What are the classes of R groups
Basic, Acidic, Polar and hydrophobic
Describe Basic R groups
- Positively charged (at pH 7)
- Hydrophilic
- Key component of their R group is an amine group
Describe Acidic R groups
- Negatively charged (at pH 7)
- Hydrophilic
- Key component of their R group is an Carboxylic acid group
Describe Polar R groups
- Hydrophilic
- Key component of their R group are hydrophilic groups like carbonyl (C=O), hydroxyl (OH) or amine (NH) groups
Describe Hydrophobic R groups
- Non-Polar
- Key component of their R group is a hydrocarbon group
Describe a Primary Amino Acid Structure
This is the sequence built during translation and is determined by the genetic code in the DNA.
(The order in which the amino acids are synthesised in the polypeptide chain)
What stabilises Secondary Amino Acid structures?
Hydrogen bonds along the backbone of the polypeptide strand (exist BETWEEN different peptide bonds)
The hydrogen bonds between different peptide bonds in a secondary amino acid structure causes…..
The peptide chain to begin to fold up into itself
What are the 3 types of Secondary Structure?
- Alpha helix
- Beta sheet
- Turns
Describe an alpha helix structure
A spiral with the R groups sticking outwards
Describe an Beta Sheet structure
Has parts of the chain running alongside each other forming a sheet. Usually anti-parallel
The R groups sit above and below the sheet
Describe a Turns structure
These reverse the direction of the chain, the exact role has not yet been determined
Describe a tertiary amino acid structure
- The final folded shape of the polypeptide
- 3D shape which contains regions of secondary structure.
- These are stabilised into a final position by interactions between the R groups of the amino acids.
How do R groups get close enough to interact in secondary and tertiary structures
The folding at the secondary level brings them close enough to interact.
Possible R group interactions in tertiary structures include…
- Hydrophobic interactions
- Ionic bonds
- London dispersion forces
- Hydrogen bonds
- Disulfide bridges (covalent bonds form between R groups containing sulfur)
What are Quaternary amino acid structures?
If proteins have more than one connected polypeptide subunit, they are said to have a quaternary structure
What is a Prosthetic Group?
A non-protein group which becomes tightly bound to a protein and is essential for its function.
For example haemoglobins ability to bind oxygen is dependent on the non-protein haem group (contains iron)
Give two factors that can influence interactions between R groups
Temperature and pH
How does Change in temperature affect R group interactions?
Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.
How does Change in pH affect R group interactions?
As pH increases or decreases from the optimum the normal ionic interaction between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.
The pH affects the charges on which R groups?
Acidic and Basic
What is a Ligand?
A ligand is very general term for anything that binds to a protein
What affect does the binding of a ligind have on the protein?
The binding of a ligand will very slightly change the shape of the protein this is a conformational change.
What happens to the R groups not used to stabilise a folding protein
They are available for ligands to bind to.
Describe Ligand binding sites on folded proteins
- created by the folding of the protein
- sites are complementary to ligind
- sites are chemically complementary to ligand
What do enzymes do?
speed up chemical reactions and lower the activation energy
What structure do many allosteric proteins have?
Quaternary
What does the binding of a ligind to an allosteric protein with multiple subunits do?
Why is this important?
Allosteric proteins with multiple subunits show co-cooperativity in binding. Meaning that changes in binding to one subunit alters the affinity of the remaining subunits.
This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.
What do modulators do?
Regulate the activity of the enzyme when they bind to the allosteric site
What happens when a modulator binds?
It changes the confirmation of the enzyme and will alter the affinity of the active site for the substrate
What are the two types of modulators?
Positive and Negative
Describe Positive modulators
Positive modulators increase the affinity for the substrate
Describe Negative modulators
Negative modulators decrease the affinity for the substrate
Describe what happens when oxygen binds to heamoglobin
Haemoglobin has four subunits, each with an oxygen binding site.
When an oxygen molecule binds to one subunit, it causes a conformational change in the other subunits, increasing their affinity for oxygen.
The affinity increases further each time an oxygen molecule binds (meaning the affinity would be highest in the fourth subunit).
Describe what happens when oxygen is released from heamoglobin
The release of an oxygen molecule from one subunit decreases the oxygen affinity in the other subunits therefore rapidly releasing oxygen into low oxygen areas such as working tissue.
Describe the affect of pH and temperature on heamoglobin and oxygen binding
This increase in temperature and lowering of pH lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.
In actively respiring tissue, this lowered affinity will promote oxygen release from haemoglobin into the tissue and provides them with the ability to continue respiring aerobically and generating larger volumes of ATP.
What is the most common post translational modification?
The addition of phosphate to particular R groups
The addition or removal of a phosphate (phosphorylation) from a protein causes …..
A reversible conformational change
The addition or removal of a phosphate from a protein is important beacuse ….
It is an important method of regulating the activity of cell processes
What is a Kinase
An enzyme that catalyses phosphorylation
What is Phosphorylation
The transfer of a phosphate from ATP to the protein
Where is the terminal phosphate transfered to and from in Posphorylation?
The terminal phosphate of ATP is transferred to specific R groups.
What is the role of phosphotases
Catalyse dephosphorylation
What affect does phosphorylation have on proteins
Activated or inhibited
How does the addition of a phosphate group affect the charge of a protein
Gives it a negative charge
What are ATPases
Transmembrane enzymes that use the phosphate from ATP to phosphorylate themselves rather than their substrate
All transmembrane ATPases are involved in …….
Active transport of ions across the membrane
