Proteins Flashcards
What are the characteristics of an endergonic reaction?
- Non spontaneous reaction.
- Free energy is absorbed.
- Change in G > 0.
What is meant by reasonance within an amino acid?
Partial double bond character between carbonyl carbon and nitrogen.
What is the Phi angle in an amino acid?
Angle between alpha carbon and nitrogen.
What is the Psi angle in an amino acid?
Angle between alpha carbon and carbon.
Number of ligands, porphyrin ring.
What are the characteristics of a deoxyhaemoglobin molecule?
- Fe2+ binds 5 ligands and has larger atomic radius.
- Fe2+ does not fit in plane of porphyrin ring.
What can a spectrophotometer be used to measure?
A pigment’s ability to absorb various wavelengths of light.
What does a ligand-binding curve display?
Plot of fractional saturation (Y) against concentration of ligand (X).
Forms a hyperbolic curve.
What condition do buffers function best under?
Within 1 pH unit of their pKa
What are the properties of an alpha helix?
- Normally right handed coil.
- tightly packed
- Side chains point out.
- Every carbonyl oxygen forms a hydrogen bond with amide hydrogen 1+4.
- 3.6 residues per turn.
Describe the properties of a beta sheet.
- Hydrogen bonds between N and O of adjacent beta strands
- Can be parallel or anti-parallel or mixed
What are reverse turns, where are they found?
- Found linking beta strands.
- Used to change direction.
What is the function of coiled coils?
To minimise exposure of hydrophobic amino acid side chains to aqueous environment.
Describe the structure of the collagen triple helix.
- 3 polypeptide chains.
- Highly conserved sequences.
- Every 3rd residue is glycine - only residue small enough.
- Lots of proline so conformationally restricted.
What are the 2 structural forms of haemoglobin?
- Deoxyhemoglobin = tense form = low affinity for oxygen.
- Oxyhemoglobin = relaxed form = high affinity for oxygen.
What does the gradient of a Hill plot depict?
= 1 (no co-operativity)
>1 positive co-operativity
What is the concerted model for co-operativity?
when [O2] is low = T state favoured
when [O2] is high = R state favoured.
Protein will transition from T to R state as O2 concentration increases.
What is the effect of 2,3 biphosphoglycerate (2,3-BPG) on haemoglobin?
- Binds more tightly to deoxy-hb (T) than oxy-Hb (R)
- BPG binds to and stabilises deoxy-Hb and so increases the P50.
Explain the occurrance of Sickle Cell Anaemia.
- Substitution mutation of glutamate to valine.
- New hydrophobic interaction between neighbouring Hb’s.
- Forms fibrous aggregates.
- Distort red blood cells to sickle shape.
(reduces half life of red blood cells so selective pressure towards as resistant to malaria).
What do they separate based on?
What are the 4 types of column chromatography?
- Gel fitration (size).
- Ion exchange (charge).
- Hydrophobic interaction
- Affinity Chromatography (specific protein interactions).
How does ion exchange chromatography separate proteins?
- Based on charge.
- Solution passed through a matrix containing charged media, proteins will bind depending on charge.
What are 2 common examples of IEX media?
- DEAE Cellulose (positive charge).
- CM Cellulose (negative charge).
What is a native protein?
Protein in its functional folded conformation.
What is screw sense?
Rotation of an alpha helix with respect to its axis.
What effects do competitive inhibitors have on Lineweaver-Burk plots?
No change in Vmax, KM increases.
What is the p50?
It is the KD when talking about concentration of O2.
Dissociation constant, [O2] required to occupy 50% of binding sites.
What is the p50 for human myoglobin?
Approx. 2 torr.
What is the p50 for human haemoglobin?
Approx. 26 torr
lower affinity than myoglobin
How much energy is released by each mole of ATP?
30kJ
How do you convert units of kJ to kcal?
Divide by 4.2
What is the concentration of water?
55.6mol per litre
What is a polyprotic acid?
A molecule that can undergo more than one ionisation, giving it multiple pKa values.
Which two amino acids have additional chiral centers besides their α-carbon atoms?
Isoleucine and Threonine
