Session 2: Proteins Flashcards
What is the isoelectric point?
The point at which the pH of a protein has not net electrical charge
What is the Henderson-Hasselbalch equation?
pH = pK + log10([base]/[acid])
OR
pH = pK + log10[deprotonated]/[protonated]
How do you get rid of log10 on one side when doing a calculation using Henderson-Hasselbalch equation?
Make the number on the other side the power of 10
eg 1 = log10([deprotonated]/[protonated]) => 10^1 = [deprotonated]/[protonated]
What is the functional importance of a positive charge on Histone proteins?
Allows them to associate with DNA which is negatively charged via electrostatic interactions to form chromatin
What is the relationship between pH, isoelectric point, and the charge if a protein?
pH < pH of isoelectric point = POSITIVE (cation)
pH> pH of isoelectric point = NEGATIVE (anion)
What does ph>pI tell us about how a protein will move in an electric field?
When pH is greater than pI = protein is deprotonated and has a negative charge so it will move towards the positive electrode (anode)
What does pH<pI tell us about how a protein will move in an electric field?
When pH is less than pI = protein is protonated and has a positive charge so it will move towards the negative electrode (cathode)
What does pH=pI tell us about how a protein will move in an electric field?
No overall net charge so protein cannot be attracted to either positive or negative electrodes so will not move
What are the characteristics of basic proteins?
- positively charged
- large proportion of positively charged amino acids (high pI)
- high pK values
- positively charged at physiological pH
Based on pH and pKa values, how can you tell if a protein will be in an acidic form & a proton donor?
When pH > pKa
Release H+
Deprotonate
Migrate towards the positive electrode
Based on pH and pKa values, how can you tell if a protein will be in a basic form & a proton acceptor?
When pH < pKa
Accepts H+
Protonate
Migrate towards negative electrode
What does pH=pKa suggest? What causes that equilibrium to shift?
Equal numbers of protonated and unprotonated groups.
pH shifts the equilibrium to either side
What does the pKa value of an amino acid side chain tell us about that chemical group?
- Likelihood for amino acid side chain will become deprotonated (release H+)
- Provides info on side chain charge & effect of pH on side chain
What are the types of bonds involved in maintaining the different levels of protein structure? What are the consequences of their disruptions
- Primary = covalent peptide bonds
- Secondary = H bonds between polypeptide backbone (amide H and carbonyl O)
- Tertiary & quaternary = different types of non-covalent forces (eg disulphide bridges, Van der Waals & ionic bonds)
Protein would turn into flexible polypeptide chain that has lost its natural shape
What are the different arrangements of beta sheet in secondary structure?
- extended beta-strand structure
- antiparallel
- mixed
- parallel
How are beta sheets stabilised?
Hydrogen bonds
Describe the structure of beta sheets.
Beta sheets are composed of adjacent beta stands
What are the features of peptide bonds which are important for protein structure?
- Planar
- Rigid => C-N has partial double bond characteristics due to delocalised electrons
- Trans conformation => carbonyl O and amide H are always on opposite sides of the peptide bond
- Bonds are free to rotate - Psi & Phi bonds
Why are peptide bonds rigid?
C-N has partial double bond characteristics due to delocalised electrons
What does the amino acid sequence of a protein determine?
- the way in which the polypeptide chain folds
- physical characteristics of a protein
What are the key properties of proteins?
Size
- number of amino acid residues
- molecular weight
Isoelectric point
What are Psi and Phi bonds?
Psi = C(alpha)-C bond
Phi = C(alpha)- N bond
What are globular and fibrous structures? How do they differ?
They are types of tertiary structures.
Globular = compact structure & made up of several types of secondary structure
Fibrous = extended conformation & made up of single type of repeating secondary structure
What is a quaternary structure?
Spatial arrangement of subunits and their interactions
What are amyloid fibres and how are they formed
Insoluble form of normally soluble protein
Due to misfolding of protein
Describe the structure of amyloid fibres.
- highly ordered with a high degree of beta-sheet
- interchain assembly stabilised by hydrophobic interactions between aromatic amino acid residue
How do proteins fold?
- Folding must be ordered (NOT random)
- Each step involves localised folding with stable confirmations maintained
- driven by the need to find the most stable conformation
Where is all the information needed for folding contained in?
Primary sequence
What happens to proteins when they denature?
- Becomes a simple polypeptide chain
- Lost structure & function
What determines how proteins can fold?
Primary sequence
How are amino acids joined together to give a sequence?
Covalent peptide bonds
What are disulphide bonds?
bonds formed between sulphydryl (SH) groups of cysteine AA residue
Why are disulphide bonds needed?
help maintain structure of molecule in harsh environment outside the cell
How can disulphide bonds be broken?
can be broken down with reducing agents like mercaptoethanol
What does pKa describe?
acid dissociation constant, the pH at which there is an equal balance of an AA in solution
