1.2 PROTEINS Flashcards
What is the Genome?
An organism’s complete set of DNA
What is the Proteome?
The entire set of proteins expressed by a genome.
Why is the Proteome larger than the Genome?
Due to alternative RNA splicing and post-translational modification
What is the result of Gene Expression?
Not all genes are expressed as proteins in a particular cell
What is the benefit of Gene Expression?
Only essential proteins are produced and therefore the cell is more energy and resource efficient
What does amino acid sequence determine?
Protein structure
What is a protein?
A polymer of amino acid monomers
Which type of bond links amino acids?
Peptide bonds
What is a chain of amino acids called?
Polypeptide
What are the four types of protein structure?
Primary, Secondary, Tertiary and Quaternary
What is the primary structure of a protein?
The sequence in which the amino acids are synthesised into a polypeptide
What is the secondary structure of a protein?
Alpha helices / Beta sheets / Turns
What causes secondary structure?
Hydrogen bonding along the backbone of the protein
What is the tertiary structure of a protein?
3D folding of the polypeptide
What causes tertiary structure?
Bonding - interactions between R groups, hydrophobic/hydrophilic interactions, ionic bonds, van der Walls interactions, disulfide bridges
What is an R group?
Functional group attached to the amino and carboxyl group compound (other component of amino acids). They are the only thing which distinguishes the 20 different amino acids.
What affects R group interactions?
Temperature and PH
Other than folding, what else is included in tertiary structure?
Prosthetic groups
What are prosthetic groups?
Non-protein unit bound to a protein which is essential for protein function
What is the quaternary structure of a protein?
Consisting of several connected polypeptide sub-units
What influences the location of proteins in cells?
Hydrophobic and Hydrophilic Interactions
What determines the location of proteins in a cell?
R groups at the surface of the proteins
What is a soluble protein?
A protein found in the cytoplasm
What do Hydrophilic R groups in soluble proteins do?
The R groups predominate at the suface of the protein
What does predominate mean?
To become the strongest or main element; greater in number
What do Hydrophobic R groups in soluble proteins do?
The R groups may cluster at the centre to form a globular structure
What is the name of membrane model we study?
Fluid mosiac model
What are the two types of membrane protein?
Integral and peripheral
Give an example of an integral membrane protein.
Transmembrane protein (eg. Channel, transporter, receptor)
What holds integral proteins within the phospholipid bilayer?
Strong hydrophobic reactions caused by regions of hydrophobic R groups
What is the difference between the R groups in peripheral and integral proteins?
Peripheral proteins have fewer hydrphobic R groups interacting with the phospholipids compared to integral proteins
What is a ligand?
A substance which can bind to a protein
What allows proteins to bind to ligands?
R groups NOT involved in protein folding can allow binding
What must ligand-binding sites have?
A complementary shape and chemistry to the ligand
What can DNA bind to?
A number of proteins
How does DNA bind to histone proteins?
Positively charged histone proteins bind to negatively charged sugar-phosphate DNA backbone in eukaryotic cells
What is the benefit of DNA binding to histone proteins?
DNA wraps around histones forming nucleosomes which pack the DNA in chromosomes
What do nucleosomes do?
They pack DNA in chromosomes
How do proteins (other than histones) bind to DNA?
They have binding sites specific to particular sequences of double-stranded DNA
What can proteins (other than histones) do when bound to DNA?
Stimulate or inhibit transcription
What is the result of a ligand binding to a protein?
Conformational change of protein
What is the result of a substrate binding to an enzyme’s active site?
Conformational change of enzyme (protein)
What is the result of a conformational change of a protein?
Functional change
What is induced fit?
A temporary change in the shape of an enzyme’s active site
What causes induced fit?
Correct substrate begins to bind to enzyme’s active site
What is the result of induced fit?
Increases the binding and interaction of the enzyme with the substrate
What is activation energy?
The minimum quantity of energy required in order to undergo a particular reaction
How do enzymes lower activation energy?
The chemical environment lowers the activation energy required
What happens after catalysis?
The original enzyme conformation is resumed and products are released from active site
What is an allosteric enzyme?
An enzyme which changes its conformation upon the binding of a modulator to a secondary binding site
What are the two types of modulators?
Positive and negative
What is the result of a modulator binding to an allosteric enzyme?
Conformational change of enzyme, altering affinity of active site for the substrate
What is the result of a positive modulator binding to an allosteric enzyme?
Increases enzyme’s affintiy for substrate
What is the result of a negative modulator binding to an allosteric enzyme?
Reduces enzyme’s affintiy for substrate
What is cooperativity?
When the binding of a ligand at one site influences binding at a second site
Which type of proteins does cooperativity affect?
Proteins with quaternary structure
What is the result of cooperativity in proteins with quaternary structure?
Binding at one subunit alters the affinity of the remaining subunits
What is the result of a haemoglobin subunit binding to a molecule of oxygen?
The second subunit binds more easily, the third even more and the fourth easier still
What is the result of an oxy-haemoglobin subunit releasing its oxygen?
The second subunit is more likely to release its oxygen and so on.
Which factors affect haemoglobin’s ability to bind to oxygen?
Temperature and pH
How does temperature affect haemoglobin’s ability to bind to oxygen?
As temperature increases, affinity for oxygen decreases
How does pH affect haemoglobin’s ability to bind to oxygen?
As pH decreases, affinity for oxygen also decreases
What can be used to cause a reversible conformational change in a protein?
The addition or removal of phosphate from particular R groups
What is the addition/removal of phosphate from particular R groups a common form of?
Post-translational modification
What is the benefit of a reversible conformational change?
Allows activity of cellular proteins to be regulated
What is a kinase enzyme?
An enzyme which catalyses the transfer of a phosphate group from ATP to another molecule
What are kinases responsible for?
Phosphorylation of other proteins
What are phosphatases responsible for?
They catalyse dephosphorylation
What are ATPases responsible for?
Using ATP to catalyse their own phosphorylation
What is myosin?
A fibrous protein which forms the contractile filaments of muscle cells
What is myosin responsible for?
Muscle contraction
What happens when ATP binds to myosin?
Myosin head detaches from actin, swings forwards and rebinds
What is the result of myosin rebinding?
ADP and a phosphate ion is released, dragging the myosisn along the actin filament
What are the four classes of R groups?
Acidic (Negative), Basic (Positive), Polar, Hydrophobic
