module 1

Question 1

what is gibbs free energy

Answer 1

is the energy of the reaction to do work “available energy”

Question 2

that is the formula for gibbs free energy

Answer 2

Delta H-(tempreature x delta entropy)

Question 3

a negative delta G is given by

Answer 3

§ Negative enthalpy (exothermic)
§ Positive entropy (increase in entropy)
Or any combination that leaves negative DeltaG

Question 4

what are stardard conditions in biochemistry

Answer 4

25 degrees
gas pressures at 101.3kpa
reactants and products of 1 M

Question 5

what happens when delta G is zero

Answer 5

it means the reaction can do no work

Question 6

how do you keep the concentration of products much lower then the reactants

Answer 6

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

Question 7

why is ATP energy rich

Answer 7

Energy is required to break any bond

Energy is released when any bond forms therefore when ATP+Pi are formed they released energy!!!!!

Question 8

what are the biological functions of proteins

Answer 8

• Catalysis
  
  • Transport
  • Structure
  • Motion
    Signalling

Question 9

what is the structure of an amino acid (components)

Answer 9

An acidic carboxyl group
A basic amino group
R group which different between the amino acids

Question 10

is the alpha carbon chiral or not

Answer 10

yes it is chairal

Question 11

how are D amino acids made

Answer 11

Made by starting synthesis of D-glyceraldehyde

Question 12

how are L amino acids made

Answer 12

Made by starting synthesis from L-glyceraldehyde

Question 13

what are the acidic amino acids

Answer 13

Question 14

what are the polar uncharged amino acids

Answer 14

Question 15

what are the non polar hydrophobic amino acids

Answer 15

Question 16

what are the aromatic amino acids

Answer 16

Question 17

what are aromatic sides responsible for

Answer 17

• 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

Question 18

what formula is used for adsorption of aromtoc amino acids

Answer 18

beer-lambert laws

Question 19

what is beer-lambert law

Answer 19

Absorption= molecular coefficient x concentration x path length

Question 20

what are disulfide bonds

Answer 20

bonds between two cysteine amino acids

Question 21

what are the two types of disulfide bonds

Answer 21

1) Interchain disulfide bonds
2) intrachain disulfide bonds

Question 22

how is a disulfide bond made

Answer 22

formed by the oxidation of Cysetine where covalent bonds are formed between two Cys amino acids

Question 23

what are the four ways to represent proteins

Answer 23

Worm/tube backbone
Ribbon backbone
Space filling heavy atoms
Line (all atoms)

Question 24

proteins are most stable when

Answer 24

Folded shape of a protein (conformation) is specified by its amino acid sequence

Question 25

what does the amino acid sequence determine

Answer 25

The amino acid sequence of a protein encodes the folded structure it will adopt

Question 26

what is the rotation like on the aminde bondand why faggot!!!!

Answer 26

* 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

Question 27

a peptide bond has 2 isomerism. what are they

Answer 27

cis and trans

Question 28

what is the most stable isomerism for the amide bond and why

Answer 28

* 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

Question 29

what is the ratio for trans amino acids

Answer 29

1000:1

Question 30

what is the ratio for protein for trans to cis for proline

Answer 30

4:1 due to steric hinderance in both the cis and trans

Question 31

what are the 3 dihedral angles

Answer 31

omega psi phi

Question 32

the omega angle is looking along the

Answer 32

C-N bond (omega) desribes the dihedral angle or "torsion angle" between the C alpha and C bond and the N-C alpha bond)

Question 33

the phi angle is looking at the

Answer 33

The bond between the N-C alpha and C-C alpha is a pure single-single double bond

Question 34

what is the psi angle looking along

Answer 34

Rotation about the Ca-C bond is described by the Psi angle

Question 35

why are phi and psi important

Answer 35

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