Biochemistry 1 (2) Flashcards
Semester 1 year 1
How is the C-C bond formed in ethane?
Formed by sigma overlap of 2 carbon sp3 hybrid orbitals
In ethane, what bond does each carbon form with hydrogen?
Sigma bond
What is a sigma bond?
Where the overlap of 2 atomic orbitals is along a line drawn between the nuclei
Can sigma bonds rotate or not?
Free to rotate around the bond axis + electron cloud in the middle of carbons will remain
Are bonds involving hybrid orbitals or ‘pure’ atomic orbitals more stable?
Bonds involving hybrid orbitals
How are sp2 hybrid orbitals made?
-2s orbital combines with only 2 of the 3 2p orbitals
-results in 3 sp2 orbitals and one 2pz orbital in its ground state
What arrangement are sp2 orbitals in?
-a planar trigonal arrangement
-3 sp2 orbitals are 120 degrees and are perpendicular to the 2p orbital
In ethene, what type of bonds are formed between the carbons and hydrogen?
-sigma bond formed between the 2 carbons (sp2-sp2 overlap)
-sigma bond formed between the carbons and hydrogens (sp2-s overlap)
What type of bonds are formed between the carbons in ethene?
-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
Describe pi bonds
-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
Describe the bonding in ethyne (C2H2)
-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
In ethyne, what arrangement are the sp hybrid orbitals in?
Linear arrangement
Describe the relationship between bond strength + bond length?
Stronger bond = shorter length
What are the bond lengths and angles in ethane?
C-C bond length = 1.54A
C-H bond length = 1.10A
Angle between C-C and C-H = 109.5 degrees
What are the bond lengths and angles in ethene?
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
What are the bond lengths and angles in ethyne?
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
What is 1A in metres?
1A = 10^-10 m
Describe polar and non-polar bonds?
-non-polar = equal sharing of electrons
-polar = sharing of electrons between atoms of different electronegativities
What is the hybridisation state of the alpha carbon in the amino acid?
sp3
What isomers can amino acids form and why?
-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
In an oxidised state, what can 2 cysteine amino acids form?
-form a disulphide bridge (S-S), forming a cysteine
-S-S bond important for structural integrity as it influences 2nd + 3rd protein structure
What are the properties of peptide bonds?
-very stable
-planar
-free rotation around the N-Calpha and Calpha-C bonds
What does free rotation around the N-Calpha and Calpha-C bonds in an amino acid result in?
-makes it flexible
-allows protein to fold in different ways
What are the bond angles between N-Calpha and Calpha-C called?
-between N-Calpha is called phi
-between Calpha-C is called psi
Why aren’t many combinations of psi + phi found in proteins?
-steric clashes between atoms
-they would occupy the same space, which isn’t possible
