Unit 1 - Cells and Proteins Flashcards
What is the proteome?
The entire set of proteins expressed by a genome
What makes the proteome larger that the genome?
Post-translational modification and alternative/RNA splicing
What is alternative/RNA splicing?
The joining of exons after introns are removed from the primary transcript
What are introns?
Non-coding regions of mRNA
What is post-translational modification?
Changes made to polypeptides following translation
Examples of post-translational modification.
Cutting the polypeptide chain and reassemble a modified version (insulin by cleavage (cutting) of proinsulin), add a functional group such as a carbohydrate or phosphate group (add carbohydrate to make glycoprotein)
What are the distinguishing features of protein molecules?
Folded nature, ability to bind tightly and specifically to other molecules (ligands)
Binding sites on the protein are complementary to the…
ligand
What does the ligand binding do to the protein?
Causes a conformational change
What does a conformational change do to the protein?
It can result in an altered function
What do all amino acids have?
A central carbon with four groups attached (an amine (NH2)), a carboxylic acid (COOH), a hydrogen and a variable R group
What does the R group on a protein do?
Determines the amino acids characteristics
Hydrophilic molecules are…
Polar
Hydrophobic molecules are…
Non polar
R groups that are positively charged are…
Basic
R groups that are negatively charged are…
Acidic
What’s the key component of a negatively charged, hydrophilic amino acid?
Carboxylic acid group
What’s the key component of a positively charged, hydrophilic amino acid?
Amine group
What’s the key component of a polar, hydrophilic amino acid?
Carbonyl, hyrdoxyl, amine groups
What’s the key component of a non-polar, hydrophobic amino acid?
Hydrocarbon group
What are the four levels of protein structure?
Primary, secondary, tertiary, quaternary
What is the primary structure of a protein?
The linear sequence of amino acids
Example of primary structure.
Insulin, shapes to bind to receptor proteins in the plasma membrane of liver muscle and fat cells
What is the secondary structure of a protein?
a-helix (alpha helix) and b-pleated (beta pleated) sheets are formed by hydrogen bonding
What type of bonding is it and where on the protein is it on secondary structure?
Hydrogen, backbone of the protein
The bond in a-helices form between what two chemicals?
N-H and C=O groups
What are the two varieties of beta-pleated sheets?
Parallel and antiparallel
What is the tertiary structure of a protein?
Final 3D shape of protein fored by interactions between R-groups
What is the difference between hydrophobic and hydrophilic amino acids in tertiary structure?
Hydrophobic cluster together in the interior of the protien. Hydrophilic predominate at the surface of the protein
What bonds are involved on tertiary structure?
Ionic (atoms are oppositely charged) , hydrogen and disulphide (covalent bond between two thiol groups) bonds
What is Van der Waals interaction?
Caused by fluctuations in elecron clouds around molecules which cause them to become slightly positively or negatively charged. May result in attraction or repulsion between atoms
What are prosthetic groups?
Non-protein parts
What do prosthetic groups do?
Give proteins added function e.g. haem in myoglobin
What is quaternary structure?
Several connected polypeptide subunits which are linked by bonds between R groups of the polypeptide chain
Give an example of quaternary structure.
Haemoglobin
What influences the interactions of the R groups?
pH and temperature
What’s the difference between integral and peripheral proteins?
Integral proteins are held within the membrane, peripheral proteins are loosely associated with the plasma membrane
What does it mean if some integral proteins are transmembrane?
They span the entire width of the membrane
Examples of transmembrane proteins.
Channels, transporters and receptors
What is a ligand?
A substance that can bind to a protein
What does the fluid mosaic model describe?
The structure of the plasma membrane
What are membranes comprised of?
A phospholipid bilayer and a patchwork of protein molecules
What are histones?
Packing proteins that DNA wraps around
How are nucleosomes formed?
When DNA is wrapped around histones
What are activator proteins?
They bind to specific DNA sequences and stimulate transcription
What is needed to allow a reaction to occur?
Activation energy
What happens to a reaction (the activation energy) when a catalyst is present?
The activation energy is lowered
In living systems, how do enzymes lower the activation energy?
By forming an enzyme-substrate complex
Describe induced fit in enzymes.
When the correct substrate binds to the enzyme a temporary change in the conformation occurs increasing the binding and interaction (affinity) with the substrate
What is an allosteric enzyme?
One which changes conformation upon binding a modulator
Where do modulators bind on an allosteric enzyme?
Secondary sites called allosteric sites
What do negative modulators do?
Reduce the enzyme’s affinity for the substrate
What do positive modulators do?
Increase the enzyme;s affinity for the substrate
How does haemoglobin show cooperativity?
When each polypeptide subunit (containing a haem group capable of binding to oxygen) the next one binds more easily and more easily. This is positive cooperativity.
What does the cooperative binding of O2 with haemoglobin do?
It allows blood to carry about 60 times more O2 than it could if O2 dissolved in the plasma
What happens to the saturation of oxyhaemoglobin when the temperture is decreased and the pH is increased?
It increases
What happens to the saturation of oxyhaemoglobin when the temperture is increased and the pH is decreased?
It decreases
What factors affect haemoglobin’s ability to bind to oxygen?
Temperature and pH
What do kinase enzymes do?
Responsible for the phosphorylation of other proteins
What do phosphatase enzymes do?
Catalyse dephosphorylation
What does the addition or removal of phosphate from particular R groups cause?
Reversible conformational changes in proteins
What is a sarcomere?
A basic unit of muscle
What proteins are in a sarcomere?
Actin and myosin
What happens during muscle contraction?
Myosin have heads that act as cross bridges as they bind to actin. When ATP binds to myosin, the myosin head detaches from actin, swings forward and rebinds. The rebinding releases the ADP and a phosphate and drags the myosin along the actin filament (power stroke)
