Lecture 1 Flashcards
What can be used to mostly infer primary structure
The DNA sequence
What are the two ways of predicting the secondary structure of a protein
Can be determined from the primary structure de novo or by alignment with other proteins of known structures using a website database
? helices are formed by hydrogen bonding within the polypeptide chain, known as intra-chain hydrogen bonding, T or F
T
What can be said about the direction of hydrogen bonds in ? helices
They are vertical hydrogen bonds
What is the major disadvantage of X-ray crystallography
Extremely expensive (£200,000 in the lab, >£300m for professional synchrotron sources)
What is meant when referring to ? helices as heptad structures
7 amino acids for every two turns of the helix
The more ordered and symmetrical the protein specimen is that is used in cryo-EM, the easier the averaging process, T or F
T
Describe the structure of a ? sheet
Beta strands are connected laterally by backbone hydrogen bonds
What is the main function of circular dichroism
Used to induce secondary structure in proteins
In what plane do the hydrogen bonds between ? sheet polypeptide chains occur
Horizontal hydrogen bonds
Which amino acid residues form hydrogen bonds with water molecules and are exposed on the outside of the proteins
Hydrophilic polar side chains
Which types of amino acids residues are found in the middle of the ? strands/sheets and give examples
Aromatic residues such as tyrosine, phenylalanine, tryptophan, valine and isoleucine
How can CD be used to infer the stability of a protein upon heating
Less stable proteins will lose its characteristic CD spectrum upon heating
Describe the structure of a triple-coiled-coil protein
Another stable structure formed by ? helices. This is where 3 amphipathic helices twist around a central axis with the hydrophobic side chains of all three exposed in the centre of the structure. This creates a stable hydrophobic core
What are the 4 different ways of representing protein structure
Sticks, space-filling, ribbon and backbone
CD gives a relative % or fraction of each of the secondary structure types in any protein by its unique spectrum, T or F
T
What two types or arrangements of ? strands in ? sheets can be observed
Parallel and antiparallel
Protein databases provide a wealth of information and predictions based on sequence alignment, domain composition, post-translational modification, protein-protein interactions and structures, T or F
T
The position of an amino acid in the primary sequence enables you to predict the secondary structure of a protein, T or F
T
Duplication and multimersiation occurs often in proteins, T or F
T
Give some examples of diseases associated with protein misfolding
Huntington’s, cystic fibrosis (CFTR), cancer (p53) and Alzheimer’s
At which terminus does protein synthesis start at
Amino-terminus
What are the different domains of the src-tyrosine kinase
Large kinase domain, small kinase domain, SH2 and SH3
What is the main advantage of NMR
The process is very dynamic and can be used to determine protein structure in solution
How can CD be used to look at changes in protein structure
CD can be used to investigate the effects on protein structure due to changes in pH and temperature. For example, increasing pH increases helix formation whilst decreasing ? sheet formation. In addition, it can be used to visualise protein unfolding due to increasing temperatures.
Two which terminus of the ? sheet do the arrows seen in ribbon diagrams point to
Carboxyl (C) – terminus
Describe how Edman degradation can be used to obtain the primary protein structure
Using phenyl isothiocyanate (PCT) to bind to and break away the terminal amino acid in a step by step process you can determine the unique sequence by high performance liquid chromatography (HPLC). This is done based on the molecular weight of each residue
Define the tertiary structure of a protein
The way in which individual secondary structural elements pack together within a protein and between sub-domains of proteins
What is the name of the enzyme responsible for catalysing the conversion of sugar(s) into ethanol and carbon dioxide often used in wine making
Zymase
Describe an ? helical structure
Spiral conformation in which every backbone amino group donates a hydrogen bond to the backbone carboxyl group of the amino acid located 3-4 residues earlier in the protein sequence
Explain how NMR can be used to determine protein structure
Specific isotopes of carbon and nitrogen (13C and 15N) are introduced into the protein of interest by growing bacteria in a medium containing nutrients with these specific isotopes only. The subatomic particles of these isotopes possess a quantum-mechanical spin. These spin vectors are aligned with a large magnetic field in a number of configurations determined by energy state. Radiowaves are then used to resonate with the natural frequency of these particles spins and cause a transition in spin vector orientation to a high energy conformation. The NMR machine then records the different frequencies required for resonance to occur. This attribute, known as chemical shift, is dependent on the local environment and can be used to determine protein structure.
Which two amino acid residues have low helix forming propensities
Proline and glycine
Give an example of a triple-coiled-coil structured protein and its role in the body
A triple-coiled-coil is the major structural theme in fibrinogen, a protein involved in blood clotting. The fibrous nature of this protein is related to its ability to form blood clots
How many sub-domains are contained in the src-tyrosine kinase
4
If a protein contains a hydrophobic centre, what is it likely to be
Soluble
Explain how X-ray crystallography can be used to infer information about protein structure
A high energy focussed beam of electrons is fired through a protein crystal. Most of these x-rays pass straight through the crystal but some are deflected back. This gives rise to a diffraction pattern that is unique to each protein. The structure of the protein can then effectively be traced back to its diffraction pattern
Define the primary protein structure
Individual linear sequence of amino acids
Describe how transmission electron microscopy can be used to infer protein structure
The protein of interest is placed on an EM grid and spiked with a solution containing a heavy metal shading that is impermeable to electrons. Electrons are then fired at the protein and a negative stain is produced. Image analysis is then employed to build-up an average structure
The hydrogen bonds that form in ? sheets form between polypeptide chain and are referred to as intra-chain hydrogen bonds, T or F
F – the hydrogen bonds do form between polypeptide chains but are referred to as inter-chain hydrogen bonds
What method other than Edman degradation (chemical disruption) can be used to infer primary structure of a protein
Physical disruption through mass spectrometry
Random coils are another secondary structure of proteins and can connect ? sheets together, T or F
T
Coiled-coils are often found in soluble proteins, T or F
F – they are often found in elongated, fibrous proteins
CD spectroscopy measures the differential absorption of linearly polarised light, T or F
F – measures the differential absorption of circularly polarised light
Lecture 1 Qn 18 Determine which representations of ? sheet protein structures the following images correspond to
Backbone, sticks, space filling, ribbon
How often do hydrogen bonds occur in the primary sequence of an ? helix
Every 3.6 residues
Describe the structure of a coiled-coil
Two ? helices wrap around eachother to form a stable structure. One side of each helix contains mostly aliphatic amino acids (such as leucine and valine). The other side contains mostly polar residues. The two helices are amphipathic and contain distinct hydrophobic and polar side chains. These two amphipathic helices align with hydrophobic residues packed tightly in the centre of the structure and polar hydrophilic faces exposed to the solvent.
How can CD be used to determine protein refolding capabilities
Cooling the protein down can be used to determine the ability of the protein to refold by seeing if it can regain its characteristic CD spectrum
What is the difference in the structures of the two kinase domains of src-tyrosine kinase
The large kinase domain is mostly ? helical in structure whereas the smaller kinase domain is mostly a ? sheet
How does cyro-electron microscopy enable the derivation of average protein shape
Vitreous ice is used to preserve/freeze the protein specimen. Electrons are then shone onto the frozen specimen and the average shape of the protein is determined.
Which amino acid residues end up in the centre of the proteins secondary structure and why is this
Non-polar side chain amino acids end up in the centre of the proteins structure forming hydrophobic core regions
How can a helical structure be implied by the amino acid composition at certain positions
Hydrophobic (leucine or valine) residues at every 4th or 5th position in the primary sequence implies a helix
What is the result of some mutations in the src-tyrosine kinase
Some sarcoma cancers
What are the major disadvantages of NMR
Expensive and is limited to proteins under 50kDa and so can often only be used on protein subdomains. Also a very high sample concentration is required as well as the incorporation of the isotope label.
What is meant by the quaternary structure of a protein
The relationship between individual proteins in a multimeric complex
CD also give information on the arrangement of proteins, T or F
F – it cannot give arrangement information
Which amino acid residues have high helix forming propensities
Methionine, alanine, leucine, lysine and glutamate
What is meant by the term secondary protein structure
Local folding of the primary amino acid sequence into three different types of structures; ? helices, ? sheets and random coils
What does the prediction of the secondary structure rely on in order to achieve desired structures
The tendency of particular amino acids to form particular structures
Explain how CD works
CD spectroscopy uses far-UV radiation (190-250nm) to reveal the secondary structures of proteins. Each type of secondary structure has a unique and characteristic CD spectrum. ? helices have two-peak spectrums at 208 and 225nm whereas, ? sheets give a single peak between 216-218nm. Random coils also have a unique CD profile
What are the regulatory domains of src-tyrosine kinase and to what do they bind to
SH2 binds to phosphorylated tyrosine residues and SH3 binds to other proteins involved in regulation
