Biochemistry 1 (2)

Question 1

How is the C-C bond formed in ethane?

Answer 1

Formed by sigma overlap of 2 carbon sp3 hybrid orbitals

Question 2

In ethane, what bond does each carbon form with hydrogen?

Answer 2

Sigma bond

Question 3

What is a sigma bond?

Answer 3

Where the overlap of 2 atomic orbitals is along a line drawn between the nuclei

Question 4

Can sigma bonds rotate or not?

Answer 4

Free to rotate around the bond axis + electron cloud in the middle of carbons will remain

Question 5

Are bonds involving hybrid orbitals or ‘pure’ atomic orbitals more stable?

Answer 5

Bonds involving hybrid orbitals

Question 6

How are sp2 hybrid orbitals?

Answer 6

-2s orbital combines with only 2 of the 3 2p orbitals
-results in 3 sp2 orbitals and one 2pz orbital in its ground state

Question 7

What arrangement are sp2 orbitals in?

Answer 7

-a planar trigonal arrangement
-3 sp2 orbitals are 120 degrees and are perpendicular to the 2p orbital

Question 8

In ethene, what type of bonds are formed between the carbons and hydrogen?

Answer 8

-sigma bond formed between the 2 carbons (sp2-sp2 overlap)
-sigma bond formed between the carbons and hydrogens (sp2-s overlap)

Question 9

What type of bonds are formed between the carbons in ethene?

Answer 9

-sigma bond forms due to sp2-sp2 overlap
-pi bond forms due to p-p overlap
-double bond between the 2 carbons –> 4 electrons shared

Question 10

Describe pi bonds

Answer 10

-sticks out of plane as it has a region of electron density above and below the internuclei axis but not along it
-weaker than sigma bond
-can’t rotate freely around the bond axis as the p orbitals won’t overlap
-can only be formed when the p orbitals line up with each other

Question 11

Describe the bonding in ethyne (C2H2)

Answer 11

-2s orbitals combine with 1 of the 3 2p orbitals, forming 2 sp orbitals + 2 p orbitals
-sigma bond between the 2 carbons (sp-sp overlap)
-sigma bonds between C and H (sp-s overlap)
-2 pi bonds between the 2 carbons (py-py and pz-pz overlap)
-triple bond between the 2 carbons

Question 12

In ethyne, what arrangement are the sp hybrid orbitals in?

Answer 12

Linear arrangement

Question 13

Describe the relationship between bond strength + bond length?

Answer 13

Stronger bond = shorter length

Question 14

What are the bond lengths and angles in ethane?

Answer 14

C-C bond length = 1.54A
C-H bond length = 1.10A
Angle between C-C and C-H = 109.5 degrees

Question 15

What are the bond lengths and angles in ethene?

Answer 15

C=C bond length = 1.33A
C-H bond length = 1.08A
Angle between C=C and C-H = 121.7 degrees
Angle between 2 C-H bonds = 116.6 degrees

Question 15

What are the bond lengths and angles in ethyne?

Answer 15

C triple bond C bond length = 1.20A
C-H bond length = 1.06A
Angle between C triple bond C and C-H = 180 degrees

Question 15

What is 1A in metres?

Answer 15

1A = 10^-10 m

Question 15

Describe polar and non-polar bonds?

Answer 15

-polar = equal sharing of electrons
-non-polar = sharing of electrons between atoms of different electronegativities

Question 16

What is the hybridisation state of the alpha carbon in the amino acid?

Answer 16

sp3

Question 17

What isomers can amino acids form and why?

Answer 17

-carbon forms tetrahedral state
-forms isomers + the mirror images aren’t superimposable
-have an L and D isomer
-natural amino acids found in L isomer

Question 18

In an oxidised state, what can 2 cysteine amino acids form?

Answer 18

-form a disulphide bridge (S-S), forming a cysteine
-S-S bond important for structural integrity as it influences 2nd + 3rd protein structure

Question 18

What are the properties of peptide bonds?

Answer 18

-very stable
-planar
-free rotation around the N-Calpha and Calpha-C bonds

Question 19

What does free rotation around the N-Calpha and Calpha-C bonds in an amino acid result in?

Answer 19

-makes it flexible
-allows protein to fold in different ways

Question 20

What are the bond angles between N-Calpha and Calpha-C called?

Answer 20

-between N-Calpha is called phi
-between Calpha-C is called psi

Question 21

Why aren’t many combinations of psi + phi found in proteins?

Answer 21

-steric clashes between atoms
-they would occupy the same space, which isn’t possible