1 Proteins Flashcards
Explain the difference between hydrophobic and hydrophilic molecules in water 1.
Hydrophilic molecules can form hydrogen bonds with water as they are polar/charged and so are attracted to water. If they can small enough they are soluble.
Hydrophobic molecules cannot form hydrogen bonds with water and so collect when in water.
Discuss the bonds important for macro molecular structure and interaction 1.2
Macromoleculuar structures have strong covalent intramolecular bonds that hold the molecule together.
Intermolecular bonds are important for macromolecular function as they allow the molecule to interact with other molecules. These bonds could be hydrogen bonds if they contain polar regions. They could be van der waal interactions if two molecules have a large surface area. Negative and positive regions of two molecules (or the same) bond electrostatically. Finally hydrophilic groups can bond as they are grouped together in the presence of water.
Explain the concept of pH, pK and buffers 1.4
pH = a measure of H+ ions in a solution = -log[H+]
pK is the pH at which a molecule will have no overall charge. pH > pK then then molecule will be protonated and vica versa.
A buffer is a solution that contains a large amount of weak base/acid and its conjugate base/ acid. If a small amount of acid/ base is added then the pH remains roughly constant e.g.
HA H+ + A-
If an acid is added to the solution (H+) then the equilibrium shifts less to produce more HA and use up H+.
If a base is added to the solution, H+ is removed and so equilibrium shifts right to create more H+.
In both cases pH remains roughly constant.
Recognise and draw the generalised amino acid structure 1.5
A central chiral carbon bonded to 4 groups: R group H atom NH2 COOH
Classify amino acids according to the properties of their side chains and explain how the charge of an amino acid is effected by pH 1.6
Amino acids can be polar (hydrophilic) or non polar (hydrophobic). They can be acids or bases (charged - these are also hydrophilic).
If the pH is less than the pKa then the molecule is likely to become protonated and become positive. E.g. Basic amino acids have a high pH and so become protonated if the pH is low making them positive.
If the pH is more than the pKa then the molecule is likely to become deprotonated and become negative. E.G. Acidic amino acids have a low pH and so become deprotonated if the pH is high making then negative.
Show how a peptide bond is formed and list its key features 1.7
OH from carboxyl group of one amino acid, reacts with H from amino group of another amino acid in a condensation reaction. It is a strong covalent bond and has a bond angle that makes the amino acid chain linear.
The peptide bonds are planar because C-N has partial double bond characteristics making the peptide bond rigid and planar. The peptide bonds are always trans as R groups would get in the way of each other.
Explain how amino acid charge can influence the isoelectric point of a protein 1.8
Isoelectric point is the pKa of a protein
If amino acids are positively charged in a neutral solution then they have accepted protons making them bases and so they will add to the protein having a high isoelectric point.
If amino acids are negatively charged in a neutral solution then they have donated proteins making them acids so they will add to the protein having a low isoelectric point.
Describe what is meant by primary, secondary, tertiary and quaternary structures of proteins. 1.9
Primary structure is the sequence of amino acids.
Secondary structure is the initial level of folding of the primary structure in alpha helix and beta pleated sheets. (Local spatial arrangement of polypeptide backbone)
Tertiary structure is the 3D shape and folding of protein.
Quaternary structure is different protein strands bonding together into a new structure/ 3D arrangement of protein sub units.
Describe the types of bonds and forces involved in protein structure and how their disruption can lead to protein denaturation. 1.10
Disulfide bonds can from between amino acid side chains and these can be broken by NADH? or heavy metal ions.
Electrostatic and hydrogen bonds can be broken by an acidic/ basic pH.
Van Der Walls and hydrogen bonds can be broken by an increase in temperature.
In each case the protein will lose part of its structure which is crucial for its function. If a protein can’t function then it is said to be denatured.
Explain the key features of the two major secondary structure elements of proteins. 1.11
Alpha helix are protein chains that spiral around each other with R groups on the outside. Each amino acid monomer forms hydrogen bonds with the monomers above and below it (every 4 amino acids) C=O and NH.
Beta strands are long strands of amino acids. They line up alongside other beta strands and form hydrogen bonds (double the amount in antiparallel) this forms beta pleated sheets.
Recognise the importance of protein folding in correct protein function. 1.12
Specifically shaped active site is needed for the protein to function often.
