KA2: Proteins: Protein structure, ligand binding and conformational change: Amino acid sequence determines protein structure Flashcards
what are proteins?
polymers of amino acid monomers
What links amino acids together to form polypeptides?
draw the link
peptide bonds
draw peptide bond
describe the basic structure of an amino acid
amine group, carboxylic acid group, variable R group
how do the R groups of amino acids vary?
*size
*shape
*charge
*hydrogen bonding capacity
*chemical reactivity
how are amino acids classed ?
name all the classifications.
according to their R groups
*basic (+charge)
*acidic (-charged)
*polar
*hydrophobic
what does the wide range of functions carried out by proteins results from?
the diversity of R groups
describe the primary sequence of a protein (mention bonds present)
involves peptide bonds which are covalent
the sequence in which the amino acids are synthesised into the polypeptide
what results in regions of secondary structure?
list the types of secondary structure.
Hydrogen bonding along the backbone of the protein strand
*alpha helices
*parallel or anti-parallel beta-pleated sheets
*turns
describe alpha helices
it is a spiral with the R groups sticking outwards
Describe the beta pleated sheet.
parts of the chain running alongside each other forming a sheet
the R groups sit above and below the sheet
what can beta-pleated sheets usually be and what does it mean?
parallel/antiparallel
the chains run in opposite directions from each other
sheets are anti-parallel or parallel depending on what?
their N and C termini
what are turns?
they serve to reserve the direction of the polypeptide chain
what is the role of turns?
-bring together and allow interactions between regular secondary structure elements
what do polypeptides fold into?
what is this conformation stabilised by?
tertiary structure
interactions between R groups:
*hydrophobic interactions
*ionic bonds
*london dispersion forces
*hydrogen bonds
*disulfide bridges
what are hydrophobic regions?
Hydrophobic amino acids do not “like” to be in contact with water.
They tend to cluster together on the interior of a protein away from the surface.
what are ionic bonds?
involves the electrostatic attraction between oppositely charged ions.
what are hydrogen bonds?
the electromagnetic attractive interaction between polar molecules, in which hydrogen is bound to a highly electronegative atom, such as nitrogen, oxygen or fluorine.
what are ldf’s?
what do they result from?
a temporary attractive force
results when the electrons in two adjacent atoms occupy positions that make the atoms form temporary dipoles.
What are disulfide bridges?
How are they produced?
covalent bonds between R groups containing sulfur
the coupling of two thiol (SH) groups.
What is a prosthetic group?
give an example
a non-protein unit tightly bound to a protein and necessary for its function
haem group
what is the ability of haemoglobin to bind to ixygen dependent upon?
the non-protein haem group
Where does the quaternary structure exist?
What does quaternary structure describe?
in proteins with two or more connected polypeptide subunits
the spatial arrangement of the subunits
what are two factors that effect R group interactions?
temperature and pH
describe how interactions of R groups can be influenced by temperature
increasing temp=> disrupts the interactions that hold the protein in shape
the protein begins to unfold, eventually becoming denatured
describe how interactions of R groups can be influenced by pH
The charges on acidic and basic R groups are affected by pH.
pH increases or decreases from the optimum=> normal ionic interactions between charged groups are lost => gradually changes the conformation of the
protein until it becomes denatured.
The secondary structure of a protein can be altered more easily than the primary structure.
Explain this in terms of the bonds involved.
bonds in primary are strong and covalent (both OR peptide)
in secondary they are weak and hydrogen (both)
The binding region of the engrailed protein contains a high proportion of lysine residues.
Suggest how the presence of these amino acids would assist in the binding of the engrailed protein to DNA.
Positive charges (of lysine) interact/bond with/attracted to the negative charges on DNA
