Unit 1 - Proteins Flashcards
What is the Proteome?
Entire set of proteins that can be expressed from a genome
What is endoplasmic reticulum?
Network of membrane tubules continuous with nuclear membrane
What is Golgi apparatus?
Series of flattened membrane discs
What are lysosomes?
Membrane bound organelles containing hydrolases that digest proteins, lipids, carbohydrates
What are vesicles?
Transports materials between membrane compartments
What is a signal sequence?
A short stretch of amino acids at one end of a polypeptide that determines the eventual location of a protein
What is post-translational modification?
Changes that occur to polypeptides after they have been synthesised
What is proteolytic cleavage?
When Inactive precursors are changed to produce active proteins
What is the R group?
Part of an amino acid that varies
What is a prosthetic?
A non-protein unit tightly bound to a protein and necessary for its function
What is co-operativity?
When changes in binding of a target molecule to one subunit of a polypeptide changes the affinity of the other subunits
What is a ligand?
A molecule which binds to a secondary site on an enzyme to alter its confirmation
What is an allosteric enzyme?
Enzyme that changes confirmation in response to a modulator
What is a positive modulator?
Molecule which increases an enzymes affinity for the substrate
What is a negative modulator?
A molecule which reduces an enzymes affinity for the substrate
What is a protein phosphatase?
An enzyme that removes a phosphate group from its substrate/catalyses dephosphorylation
What is a protein kinase?
A molecule which catalyses the transfer of a phosphate group to other proteins
What is genomics?
The study of the genome
What is the genome?
The total genetic material in a cell
Why is the proteome larger than the genome?
More than one protein can be produced from a single gene as a result of alternative gene splicing
What are genes that don’t code for proteins called?
Non-coding RNA genes
Examples of non-coding RNA genes?
tRNA, rRNA
Factors that affect the set of proteins expressed
- Metabolic activity
- Cellular stress
- Response to signalling molecules
What increases the total area of the membrane?
System of internal membranes
What are other structures in eukaryotes that have a membrane?
- Endoplasmic reticulum
- Golgi Apparatus
- Lysosomes
- Vesicles
What are the 2 types of endoplasmic reticulum
- Rough (ER)
- Smooth (ER)
What is the difference between smooth (ER) and rough (ER)?
Rough (ER) has ribosomes on its cytosolic face while smooth (ER) lacks ribosomes
What are membranes made up of?
Lipids and proteins
Where are lipids synthesised?
Smooth (ER) and inserted into its membrane
Where does synthesis of all proteins begin?
Cytosolic ribosomes
Where is synthesis of cytosolic proteins completed?
Cytosolic ribosomes
Where do cytosolic proteins go once synthesised?
Remain in cytosol
How are transmembrane proteins synthesised?
- Carry signal sequence, halts translation at cytosolic ribosome
- Directs ribosome to dock in ER, forming RER.
- Translation continues after docking
- Protein is inserted into membrane of RER
What happens after proteins are synthesised at the Rough (ER)?
-Transported by vesicles that bud off ER
-Fuse with Golgi apparatus
What happens when proteins move through Golgi apparatus?
Undergo post-translational modification.
What happens after post-translational modification?
Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes.
What are examples of secreted substances?
- Peptide hormones (insulin)
- Digestive enzymes (trypsin)
What is the pathway of secreted substances?
- Translated in ribosomes on RER, enter its lumen
- Bud off RER in a vesicle and go to Golgi Apparatus
- Packaged into secretory vesicles
- These vesicles move to and fuse with plasma membrane, releasing them out of the cell
What are many secreted proteins synthesised as?
Inactive precursors ( require proteolytic cleavage to become active )
What functional groups do all amino acids contain?
- Amine group
- Acid group
Categories of R-groups
- Polar
- Hydrophobic
- Acidic
- Basic
What is the acidic R group?
Contains a carboxylic acid side chain (-COOH)
What is the basic R group?
Contains an amino side chain (-NH2)
What is a polar R group?
They are hydrophilic, meaning they seek contact with aqueous solutions
What are hydrophobic R groups?
Also known as non-polar, they avoid contact with liquids
What are amino acids linked by?
Peptide bonds
What is the primary structure?
The sequence in which the amino acids are synthesised into the polypeptide
How is secondary structure formed?
Hydrogen bonding along the backbone of the protein
What are the 3 types of secondary structure?
- Alpha helix
- Beta sheets
- Turns
What is an alpha helix?
Spiral with R groups sticking out
What are Beta sheets?
Parts of polypeptide chain which run along side each other to form corrugated sheet with R above and below ( can be antiparallel and parallel )
What are turns?
They reverse the direction of the polypeptide chain and the chain folds back on itself
What is the tertiary structure?
The final folded shape of the polypeptide.
How is the tertiary structure stabilised?
Interactions of amino acids
Examples of R group interactions
- Hydrophobic interactions
- Ionic bonds
- London dispersion forces (LDFs)
- Hydrogen bonds
- Disulphide bridges
When does quaternary structure exist?
Proteins with two or more connected polypeptide subunits which are linked by bonds between 2 or more polypeptide chains
What does the quaternary structure describe?
The spatial arrangement of the subunits
What effect does increasing temperature have on R groups and structure of protein?
- Disrupts the interactions that hold proteins in shape
- Protein unfolds and becomes denatured
What effect does increasing PH have on R groups and structure of protein?
- Interactions are lost
- Changes conformation of protein until it becomes denatured
What happens when a ligand binds to a protein?
Changes the conformation of the protein which causes a functional change in the protein
What do modulators do?
Regulate the activity of the enzyme when they bind to the allosteric site
What effect does decreasing pH/increasing temperature have on haemoglobin and oxygen?
Lowers the affinity of haemoglobin for oxygen, so binding of oxygen is reduced. (in actively respiring tissue, this will promote increased oxygen delivery to tissues).
What is phosphorylation?
When a phosphate group is added to the protein
What can phosphorylation do to a protein?
Can cause reversible conformational changes in proteins
The ___________________ of ATP is transferred to specific R groups (Protein Kinases)
Terminal phosphate
What is phosphorylation a method of in many cellular proteins?
Regulation
What does adding a phosphate group do to the charge and bonds?
Adds a negative charge, Ionic interactions can be disrupted and new ones created
