Baker - proteins

Question 1

define orbital

Answer 1

region of space where an electron is likely to be found

Question 2

what is pauli’s extension principle?

Answer 2

only 2e- may be places in each orbital and must have opposite spin

Question 3

what is hund’s rule?

Answer 3

if 2+ orbitals of equal energy are available, 1e- must be placed in each orbital until they are all half filled

Question 4

what is a wave function?

Answer 4

a function describeing the probability of a particles quantum state as a function of position, momentum, time and/or spin

Question 5

what is orbital hybridisation?

Answer 5

when orbitals mix to form a new atomic orbital (holds same no of e-)

Question 6

what is asigma bond?

Answer 6

the direct overlap between orbitals between bonding atoms

Question 7

what is a pi bond?

Answer 7

the sideways overlap of adjacent p-orbitals, above and below bonding C-atoms

Question 8

what do a double and triple bond consist of?

Answer 8

double: one sigma and one pi bond
triple: one sigma and 2 pi bonds

Question 9

what is the difference in orbital organisation in ground state and excited state carbon? what is the significance of this?

Answer 9

ground state: 2e- in s orbital and 2e- in p orbitals
excited state: 1e- in s orbital and 3e- in p orbitals
carbon can now form 4 bonds instead of 3 (excited state requires energy to be formed but when bonded state is reach energy is released)

Question 10

which orbitals are involved in sp3, sp2 and sp hybridisation? give an example of a chemical that uses each type of bonding

Answer 10

sp3: 3 p orbitals and 1 s orbital - methane
sp2: 2 p orbitals and 1s orbital - ethene
sp: one p and one s orbital - ethyene

Question 11

what shape are the orbitals in sp3, sp2 and sp hybridisation? give their bond angles

Answer 11

sp3: tetrahedral - 109.5
sp2: trigonal planar - 120
sp: linear - 180

Question 12

what bond angles are present in water and ammonia?

Answer 12

water: 104.5
ammonia: 107.3

Question 13

are proteins made up of D-a/a’s or L-a/a’s

Answer 13

L-a/a’s (spells corn (ignoring the H) clockwise)

Question 14

what linkage is present in a protein

Answer 14

peptide/amide link

Question 15

name 4 properties of peptide bonds

Answer 15

v stable
partial double bond character (can’t rotate due to resonance structures)
sp2 hybridisation
planar (alpha c’s all in same plane)

Question 16

are most proteins cis or trans? why?

Answer 16

trans - avoids steric clashes in R groups

Question 17

describe what a ramachandran plot is

Answer 17

a ramachandran plot plots the angles at which there are no steric clashes. there is free rotation around the N–C alpha bond (phi) and the C alpha–C bond (psi)

Question 18

how is a disulphide bond made and why is it used?

Answer 18

its a covalent bond between S atoms in 2 cysteine residues
requires oxidative conditions
usually found in extracellular domains of proteins - confers extra stability in harsh conditions

Question 19

describe the anfinsen experiment

Answer 19

denatured native ribonuclease (has 8 cys residues = 4 disulphide bonds). then the denatured reduced ribonuclease was oxidised and the enzyme activity returned - shows oxidative conditions needed for disulphide bond formation

Question 20

give the equation to work out the energy of association for ionic bond formation (coulomb’s law)

Answer 20

E=(k(q1-q2))/Dr 
k = permittivity of free space (how easy it is for an electric charge to pass through a medium = 9 × 10^9 N⋅m2⋅C−2) 
q1/q2 = 2 electric charges
D = dielectric constant of medium
r = distance between the 2 charges

Question 21

where in a protein are ionic bonds usually found? do ionic bonds significantly stabilise proteins?

Answer 21

in the exterior, not interior - this is because polar environments disrupt ionic charges. ionic bonds are strong but they dont significantly stabilise proteins due to other interactions.

Question 22

describe the hydrophobic effect

Answer 22

The hydrophobic effect is the name given to those influences that cause nonpolar substances to minimise their contact with water, and amphipathic moleclues, such as soaps and detergents, to form micelles in aqueous solutions.

Question 23

describe the relationship between water cage formation and entropy

Answer 23

non-polar molecules bind to each other to minimise the interaction of their hydrophobic regions with water. Water forms cages around these molecules. therefore when the molecules bind together the surface area decreases and water is released from the water cage. This increases the entropy of solution.

Question 24

describe the properties of an alpha-helix (rise, rotation, hydrogen bonding pattern)

Answer 24

coiled (R-handed)
C=O and N-H H-bonding (follows i to i+4 H-bonding pattern)
1.5A rise per residue (100 degree rotation)
3,6 residues per turnn
5.4A pitch
all side chains point away and down
all main chain atoms have Van der Waals
amphiphilic in globular proteins and transmembrane proteins (can also be hydrophobic)
forms a macrodipole - dipoles of peptide bonds aligned

Question 25

describe the properties of an beta sheet

Answer 25

constructed from 2+ polypeptide strands H-bonded to each other
can be a mix of antiparallel and parallel strands
side chains of consecutive residues are on opposite sides of the sheet
sheets can be flat or twisted
Beta turn required to turn the sheet
H-bonds between CO residue i and NH of residue i+3

Question 26

name a supersecondary structure

Answer 26

beta barrel

Question 27

define a domain

Answer 27

peptide chains of ~200+ residues often fold into globular domains
these are structurally independent units with characteristics of small gobular proteins
each domain in a protein has a different function

Question 28

name four methods of post-translational modifications of amino acids

Answer 28

phosphorylation (on OH group of Ser/Thr/Tyr)
glycosylation (on Asn residues - increases hydrophilicity)
hydroxyproline (OH added to proline - stabilises collagen fibres - lack of vit C inhibits this)
gamma-carboxyglutamate (lack of this leads to haemorrhage)

Question 29

name 3 members of the serine protease family

Answer 29

chymotrypsin
trypsin
elastase

Question 30

what does glutamate dehydrogenase do?

Answer 30

glutamate + NAD+ + H2O –> alpha-ketoglutarate + NH4+ + NADH + H+

Question 31

describe the structure of glutamate dehydrogenase

Answer 31

hexamer - each subunit has 2 domains

Question 32

where do reactants bind in glutamate dehydrogenase?

Answer 32

glutamate binds the cleft between the 2 domains, NAD+ binds one domain

Question 33

how does glutamate dehydrogenase catalyse its reaction?

Answer 33

clefts close, excluding water from AS. this brins the C-alpha of Glu and and C4 of NAD nicotinamide ring closer together