Biochemistry semester 1 Flashcards
What is Hunds Rule?
When 2 or more orbitals of equal energy and available electrons will be placed in turn into each orbital until they are both half filled.
What is hybridisation?
Combining of two pure atomic orbitals to make a new orbital which is more stable than pure atomic orbitals.
What does more s character in a bond correlate too?
More s character means that the bond is shorter, stronger and has a larger bond angle.
Do L and D isomers of amino acids have the same stability?
Yes, although all naturally occurring amino acids are L isomers.
What bond angles can rotate in a peptide bond?
Alpha Carbon - N and Alpha Carbon - C
Where are disulphide bonds normally found?
The extra cellular domains of proteins where they confer stability.
In the Anfinsen experiment what was the purpose of urea?
It weakened the covalent bonds
In the Anfinsen experiment what was the purpose of B - metcaptoethanol?
It reduces the disulphide bonds.
What is the Levinthal paradox?
The Levinthal parodic states that due to the large amount of degrees of freedom there are an astronomical amounts of possible conformations of a protein.
Where are ionic interactions strongest and why?
In the core of a protein due to the low dielectric constant.
What is the VDW contact distance?
r^-6
Do ionic forces or permenant dipoles greatly stabilise a protein?
Permenant dipoles although they are weaker.
What causes London Dispersion forces?
Non polar small dipoles at the VDW contact distance.
Are hydrogen bonds longer or shorter than covalent bonds?
Longer, so electronegative atoms are kept apart.
When are hydrogen bonds strongest?
When they are linear, for example in DNA. (The donor hydrogen will be along the acceptors lone pair orbital).
Are glutamate and aspatarte hydrogen donors or acceptors?
Acceptors.
Are lysine and arginine hydrogen donors or acceptors?
Donors.
Where are the most hydrogen bonds found in proteins?
Between two main chain atoms.
Why is water not a typical solvent?
- Has a high dielectric constant.
- Low compressibility.
- High specific heat capacity.
- High surface tension.
- High enthalpy of vaporisation.
Does water stabilise non polar substances?
No.
Why does S increase as the protein folds?
Water molecules in caged structures are released.
What drives protein folding?
Non covalent forces of attraction and repulsion.
What is the strongest non covalent interaction in aqueous medium?
Hydrogen bond.
In an alpha helix are all main chain CO and NH groups hydrogen bonded?
Yes.
In an alpha helix hydrogen bonds forms between the CO and the NH group ___ places in front.
4
How can longer alpha helices form?
Multiple helices can intertwine. Normally an alpha helix can not be more than 45A in length.
Are alpha helices left or right handed?
Right.
Do helices carry a macro dipole?
Yes, the amine end is positive.
How many residues are there per turn in an alpha helix?
3.6
What degree of rotation is there per turn in an alpha helix?
100
What is the rise in an alpha helix?
1.5A
Are helices amphiphilic?
Yes, but in a transmembrane protein it can also all be hydrophobic.
What angle are antiparallel beta sheets found at?
90 degrees.
What angle are parallel beta sheets found at?
Slightly offset.
Why do beta sheets sometimes adapt a twisted shape?
There can be steric repulsion in the backbone and side chain atoms.
How is a beta turn achieved?
A hydrogen bound between a CO and NH group which is 3 places ahead.
Why would a beta turn need to be achieved?
When a universal change in direction is required.
What is the Pauli Exclusion Principle?
That each orbital can hold two electrons with opposite spin
Name three examples of super secondary structure.
B-A-B unit
B hairpin
A-A motif
How long does an amino acid chain need to be to form domains?
At least 200 residues.
What occupies the cleft between domains?
Binding sites
How many layers of structure are found in domains and why?
2+ to bury hydrophobic residues.
What is the immunoglobulin fold held together by?
Disulphide bridges.
What is the immunoglobulin fold compromised off?
Antiparallel beta sheets surrounding a hydrophobic core.
What makes up the quaternary structure?
More than one polypeptide chain associated non covalently.
What type of tetramer is heamoglobin?
2a2b
What is an Oligomer?
A monomer whose molecules consist of relatively few repeating units.
What is an allosteric interaction?
When the binding of a ligand to one unit can affect the affinity of the ligand to the other unit.
What are post translational modifications?
Covalent modification of amino acid side cabins.
What type of group is
Phosphorylated?
Hydroxyl groups
Is phosphorylation reversible?
Yes
Glycosalation acts on which molecules?
Proteins that have been secreted.
What amino acid is often involved in glycosalation?
Asparagine
What does glycosalation allow?
An increase in hydrophilicity.
What is the post translational modification of proline called and what is it’s purpose?
Hydroxyproline
It strengthens newly formed collagen fibres, also preventing scurvy.
Y- Carboxyglutamate acts on residues in which molecule?
Prothrombin
Lack of which vitamin results in insufficient carboxylation of glutamate molecules?
Vitamin A
Protein families have similar amino acid sequences and structure, but different what?
Substrate affinity.
What is the serine protease family made up off?
Chymotrypsin, trypsin and elastase. All of these have an almost identical 3D structure.
What can give a protein extra function?
Tightly bound molecules.
What is the definition of a supersecondary structure?
The packaging of secondary structure elements into local modules.
What is the definition of a domain?
The assembly of part of a polypeptide chain into a compact globular structure, often with a specific function.
What is a nucleophile?
An electron donor.
What is an electrophile?
An electron acceptor.
What effect does nucleophilic substitution have on a molecule?
It inverts chirality.
What does glutamate dehydrogenase allow?
The oxidative deamination of glutamate into alpha- ketoglutamate.
How many subunits does glutamate dehydrogenase have?
6 - it is a hexamer.
Each subunit has 2 domains and a cleft between these to bind NAD+.
What stabalises the pyro phosphate group on NAD+?
A helix dipole.
Why do the two domains move closer together during the reaction in glutamate dehydrogenase?
To exclude bulk water from the active site.
What is brought closer together when the two domains move closer together in the reaction involving glutamate dehydrogenase?
The alpha carbon on glutamate and the nictinamide ring in NAD+.
In Glutamate dehydrogenase, which amino acid abstracts a proton from the glutamate amine group?
ASP165.
This allows hydride transfer from CA to C4 on the nicinamide ring.
What two amino acids stabilise the glutamate side chains on the enzyme surface in glutamate dehydrogenase?
SER380 and LYS89.
What is the purpose of LYS113 in glutamate dehydrogenase?
It stabilises the carbonyl group on the glutamate.
What is the purpose of LYS125 and GLN in glutamate dehydrogenase?
They trap the water molecule.
Why do the two domains open at the end of the reaction with glutamate dehydrogenase?
So LYS and ASP can become deprontated again.
When the domains come together in glutamate dehydrogenase does the reaction have to occur?
No.
Why can aspartate not fit into the active site of glutamate dehydrogenase?
It is shorted by CH2.
When the a-ketoglutarate packs against the proteins surface it can only be attacked by the ammonia on one side, what does this result in?
Only L isomers of glutamate are formed.
What would not occur if bulk water was not excluded in glutamate dehydrogenase?
Hydride transfer to NAD+.
What does pKa equal?
-log(ka).
Water is a weak ___?
Nucleophile.
What does a molecules ionisation state depend on?
The pKa of it’s functional groups.
What can greatly influence side chain pKa?
The environment.
Why can amino acids be used as buffers?
They are polyprotic.
When is a molecule deprotonated?
pH > pI
When does histidine become protonated?
pH of around 6.
What is the Henderson- Hasselbach equation?
pH= pKa + log (A-/HA)
Enzymes enhance reactions by ______ and ______ effects.
Orientation, Proximity.
What speed do enzymes increase the reaction rate too?
10^8 to 10^12.
What do enzymes prefer to bind?
Translation states?
What does binding to transition states to an enzyme do to the energy barrier?
It reduces it.
Can transition states be isolated?
No.
Do enzymes bind tightly?
No.
Can enzymes undergo conformational change?
Yes.
The induced fit theory is:
Substrate ______ to enzyme ______
Stressed, strained.
What is a metalloenzyme?
When a metal is tightly associated to an enzyme.
Includes Fe, Cu, Zn
What does it mean if an enzyme is metal activated?
A metal is loosely associated with the enzyme.
Eg
Ca, Mg
What 4 things can metal ions participate in enzyme based reactions?
- They can stabilise transition state charge without effecting pH.
- They can generate nucleophilic species.
- They can increase binding interactions, such as Mg 2+ with ATP.
- Metal oxidation state changes can facilitate catalyst.
What is an Apoenyzme?
An enzyme with no cofactor bound.
What is a haloenzyme?
An enzyme with a bound cofactor:
In NAD where does hydride transfer occur?
The nicinamide ring, which has a positive charge despite the whole charge being negative.
What are oxidoreductase enzymes also known as?
Dehydrogenase.
What process do transferase enzymes assist with?
Nucleophilic substitution reactions.
Hydrolyses are a sub group of which other enzyme?
Transferases.
Lysases/ synthases do what?
Add or remove groups to form a double bond.
What is the purpose of isomerases?
Allow interconversion of isomeric forms of compounds.
Do ligases require chemical energy?
Yes.
What are ligases also known as?
Synthetases.
How many domains are in the IG fold?
12
8 in heavy
4 in light
How many heavy and light chains are there in the IG fold?
2 of each.
What is an isoprenoid?
Steroid cholesterol and lipid vitamins.
What effects the physical properties of a fatty acid?
Chain length and presence of double bonds.
What defines the phospholipid type?
The alcohol attached to the phosphate group.
Glycerol is a _____ _____ molecule.
Small, central.
What type of linkage do plasmalogens use?
Vinyl - ether.
What is a shingolipid?
An amide bond to another fatty acid.
What allows self sealing of a membrane?
Diffusion along the plane?
How much slower is diffusion across the membrane compared to diffusion along the plane of the membrane?
10^9
How is cholesterol distributed in the membrane?
Evenly.
What influences membrane curvature?
Phospholipid head size and the segregation of lipids.
What shape are phosphatidyl chlorines?
Fairly flat.
What shape are phosphatidyl ethanol amines?
Curved or cone shaped.
What determines membrane fluidity?
Fatty acid and cholesterol content.
How do bacteria regulate membrane fluidity?
Altering number of double bonds and fe length of the fatty acyl chain.
What helps with membrane straightening?
Cholesterol.
What are liposomes used for?
Experimental tools and delivery systems.
What is the percentage composition of membranes?
10% carbohydrate
25-50% lipid
50-75% protein
Varies between membranes.
What is the purpose of a FRAP experiment?
Quantifies lateral movement of membranes.
What are intristix membrane proteins also known as?
Integral.
What are extrinsic membrane proteins also known as?
Peripheral.
How can you remove an integral membrane protein from a membrane?
Detergents.
How embedded is an integral membrane protein?
Can be partially or fully embedded.
What do peripheral membrane proteins associate with?
Integral proteins or associated with the lipid head group.
How can you dissociate a peripheral membrane protein from the membrane?
Detergent or a salt wash.
How do you remove anchored membrane proteins?
You have to remove the anchor.
What type of tails to anchored membrane proteins have?
Greasy with ester or amide linkages. The side chains give it this property.
What is a GPI protein?
Anchored protein with a bigger and bulkier group and the hydrophobic tail in the membrane. The c terminus is linked.
What do transmembrane proteins often use to span the membrane?
Alpha helices.
What does a low value on a hydropathy plot show?
Wants to be in a hydrophilic environment.
What does a high value on a hydropathy plot show?
What’s to be in an hydrophobic environment.
Where in channels are hydrophobic residues found?
The middle.
What do pores transport across the membrane?
Ions.
What is an example of a primary energy source?
ATP
What is an example of a secondary energy source?
Coupling to a proton gradient.
What is the energy an object has due to it’s position called?
Potential energy.
What is the equation for work done?
Force applied x distance moved.
Objects will move to ________ potential energy.
Decrease.
What most the total kinetic energy and potential energy be?
The same.
What is the formula for kinetic energy?
1/2 x mass x speed^2
What does the Boltzmann distribution show?
That when the potential energy is low there is a high likelihood of the molecule being in that position.
Most energy transferred by collisions is equal too?
KbT
What happens to the potential energy as a protein unfolds?
It increases.
Why is protein unfolding unlikely?
It requires a lot of unfavourable conditions.
What does lots of ‘u’ states of a protein means…
There is high entropy.
What are ‘F’ and ‘U’ ?
Macrostates.
What does free energy take into account?
The number of microstates and the likelihood of microstates.
What is the equation for ‘S’?
Kb x loge(N)
What do all mixed microstates have?
An equal likelihood.
When there is a high concentration of molecules in one place is the entropy low or high?
Low.
In a mixed and separated mixture what is the pe?
The same.
Na x Kb = ?
R.
Delta G : A -> B (one mole) =?
RTloge(b/a).
If b/a is less than one will be spontaneous.
What does mass action ratio represent?
Concentrations when equilibrium is not met.
In a dead cell do all processes end up in equilibrium?
Yes.
Is entropy independent of concentration?
Yes, can have intermolecular configurational entropy.
If the number of products does not equal the number of reactants what unit must delta G be in?
Molar.
What does deltaG equal when not at equilibrium?
DeltaG0 +RTln( P1P2 / R1R2)
OR
RTln( mass action ratio/ K)
What does delta G equal at equilibrium?
0
Why are H+ ions pushed through the channel?
It will be repelled by H+ and pulled though by anions.
What is pe proportional too?
The charge of the object moved.
What is the equation for energy change (joules)?
Charge on object (columbs) x PD (volts)
