module 1 Flashcards
what is gibbs free energy
is the energy of the reaction to do work “available energy”
that is the formula for gibbs free energy
Delta H-(tempreature x delta entropy)
a negative delta G is given by
§ Negative enthalpy (exothermic)
§ Positive entropy (increase in entropy)
Or any combination that leaves negative DeltaG
what are stardard conditions in biochemistry
25 degrees
gas pressures at 101.3kpa
reactants and products of 1 M
what happens when delta G is zero
it means the reaction can do no work
how do you keep the concentration of products much lower then the reactants
Remove one or more of the products at a rate which is faster then it is produced then the reaction is now kinetically driven
Replenish one or more of the reactants at a rate which is faster then it is removed
why is ATP energy rich
Energy is required to break any bond
Energy is released when any bond forms therefore when ATP+Pi are formed they released energy!!!!!
what are the biological functions of proteins
- Catalysis
- Transport
- Structure
- Motion
Signalling
what is the structure of an amino acid (components)
An acidic carboxyl group
A basic amino group
R group which different between the amino acids
is the alpha carbon chiral or not
yes it is chairal
how are D amino acids made
Made by starting synthesis of D-glyceraldehyde
how are L amino acids made
Made by starting synthesis from L-glyceraldehyde
what are the acidic amino acids
what are the polar uncharged amino acids
what are the non polar hydrophobic amino acids
what are the aromatic amino acids
what are aromatic sides responsible for
- Aromatic side chains are responsible for most ultralight absorbance and fluorescence properties of proteins
- This is useful in protein detection
These properties are however sen
- This is useful in protein detection
what formula is used for adsorption of aromtoc amino acids
beer-lambert laws
what is beer-lambert law
Absorption= molecular coefficient x concentration x path length
what are disulfide bonds
bonds between two cysteine amino acids
what are the two types of disulfide bonds
1) Interchain disulfide bonds
2) intrachain disulfide bonds
how is a disulfide bond made
formed by the oxidation of Cysetine where covalent bonds are formed between two Cys amino acids
what are the four ways to represent proteins
Worm/tube backbone
Ribbon backbone
Space filling heavy atoms
Line (all atoms)
proteins are most stable when
Folded shape of a protein (conformation) is specified by its amino acid sequence
what does the amino acid sequence determine
The amino acid sequence of a protein encodes the folded structure it will adopt
what is the rotation like on the aminde bondand why faggot!!!!
- Peptide bonds have limited rotation
§ The peptide bonds has a partial double bond character due to resonance
§ As a result the CO-NH bond is not free and the groups are co planar
§ As a result there is 40% resonance structure double bond character
a peptide bond has 2 isomerism. what are they
cis and trans
what is the most stable isomerism for the amide bond and why
- The trans form is favoured energetically due to less steric hinderance
-Due to severe less steric hinderance (van de waals repulsion) of the side chains in cis
what is the ratio for trans amino acids
1000:1
what is the ratio for protein for trans to cis for proline
4:1 due to steric hinderance in both the cis and trans
what are the 3 dihedral angles
omega
psi
phi
the omega angle is looking along the
C-N bond (omega) desribes the dihedral angle or “torsion angle” between the C alpha and C bond and the N-C alpha bond)
the phi angle is looking at the
The bond between the N-C alpha and C-C alpha is a pure single-single double bond
what is the psi angle looking along
Rotation about the Ca-C bond is described by the Psi angle
why are phi and psi important
phi and psi are important because: assuming all peptide bonds are trans all conformational freedom in the backbone of a polypeptide is due to these rotations. Eveything else in this diagram is fixed
