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78 - Chemical Bonding

78 - Chemical Bonding

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Chemical Bonding in Biological Molecules
B io F actsheet
September 2000Number 78
1
The contents of this Factsheet are directed towards AS levelcandidates. By studying this factsheet students should gain aknowledge and understanding of:
glycosidic bonds in carbohydrate structure.
peptide bonds in polypeptide structure.
ester bonds in lipid structure.
hydrogen bonding.
sulphur bonding.
phosphate bonding.Introduction
Glycosidic, peptide and ester bonds are formed by a process called
condensation
. This is the joining of molecules by the removal of water andinvolves removing a hydroxide group from one of the molecules and ahydrogen from the other molecule. This type of reaction is important insynthetic processes. The reverse process, involved in digestion, is
hydrolysis
which is the splitting of molecules by the addition of water.
Glycosidic bonds
These are the bonds which join single sugars (monosaccharides) together toform double sugars (disaccharides) and multiple sugars (polysaccharides).The formation of a glycosidic link is shown in Fig 1.By adding more alpha-glucose molecules on at positions X and Y thebackbone molecules of starch( alpha-amylose) and glycogen may be builtup. Alpha-amylose can be between 300 and 3000 alpha-glucoses long. Theother component of starch is amylopectin. This is similar to alpha-amylosebut is branched about every twentieth glucose by a
1,6 glycosidic branchlink
. Glycogen has a structure similar to amylopectin but branches morefrequently at about every twelfth glucose.The reactive – OH group on carbon 1, labelled Y, is a reducing group and sogives the glucose reducing properties. (the power to donate hydrogen orelectrons to other substances). In alpha-glucose this group is below the ringstructure and during polymerisation forms
1,4 alpha-glycosidic bonds
.These can be hydrolysed by alpha-amylase enzymes, for example, salivaryand pancreatic amylases in mammals and diastase in seeds, and so moleculessuch as starch and glycogen can be digested to maltose and then by maltaseenzyme to glucose. The structures of alpha-amylose and amylopectin areshown in Fig 2.
Fig 1. Formation of a glycosidic link
CCC
C
OCOHHOHHHHCH
2
OHH
HO
OCC
C
COC
OH
HOHHHHCH
2
OHH
OH
alpha-glucosealpha glucose
CCC
C
OCOHHOHHHHCH
2
OHHHOOHCC
C
COCOHHOHHHHCH
2
OHHHOOH+
carbon 1carbon 4XY
1,4 alpha-glycosidic link alpha-maltosecondensationhydrolysis
Fig 2. Structure of alpha-amylose and anmylopectin
OOOOOOOOOOO
ααααα
- amylose
1,4 glycosidic
α
- link 
OOOOOOOOOOOOOOOOOOCH
2
1,6 glycosidic branch link 
amylopectin
+ H
2
O
Exam Hint 
- Candidates will be expected to recognise and name molecules and bonds but will not be expected to write down structural formulae from memory. Candidates may be asked direct questions about types of bonds, or may need to refer to the different bond types in essay answers.
 
Chemical bonding in biological molecules
Bio Factsheet
2
Enzymes for breaking down the 1,6 glycosidic branch links are not presentin most animals and so amylopectin (and glycogen) can only be digested byamylases down to the branch points. This leaves an indigestible residue of amylopectin, which is called dextrin. Cooking will hydrolyse the 1,6glycosidic links and thus cooked starch can be completely digested.In beta-glucose the reducing –OH group lies above the ring structure andwhen glycosidic bonds form they are
1,4 beta-glycosidic bonds (links)
.These are found in the structural compound, cellulose. The formation of abeta-link is shown in Fig 3.
Fig 3. Formation of a 1,4 beta-glycosidic link
βββββ
-glucoses
CCC
C
OCOHHOHHOHHCH
2
OHHHOHCC
C
COCOHHOHHOHHCH
2
OHHHOH+
condensationsynthesishydrolysisdigestion
CCC
C
OCOHHOHHHCH
2
OHH
HO
HCC
C
COCOHHOHH
OH
HCH
2
OHHHOH
2
O +
A
1,4 glycosdic beta link 
Cellobiose
More beta glucoses can be added, on by condensation, to the disaccharidecellobiose at points A to build up a long unbranched cellulose molecule.Cellulose molecules run together in parallel fashion to form cellulose fibrils.Within a fibril the adjacent cellulose molecules cross link by
hydrogenbonds
. (Hydrogen bonds are described below). Individually such bondsare weak but their presence in large numbers gives strength which makescellulose a good structural material in plant cell walls.Very few animals possess cellulase enzymes capable of hydrolysing betaglycosidic links and so cellulose is usually indigestible. Many fungi andbacteria possess cellulases and are important in breaking cellulose down inrotting vegetation in the soil. The microbes in the rumens of cow and sheepalso possess cellulases and so can break down the cellulose in the grass thatthese animals eat.
Formation of peptide bonds
Peptide bonds are formed by condensation between the acid group of oneamino acid and the amine group of another amino acid. They enable aminoacids to be joined into long chains called polypeptides. Fig 4. shows theformation of a dipeptide from two amino acids.
Fig 4. Formation of a peptide bond
H
2
NCRHC
OH
CONCRHCOOH
H
H
+condensationsynthesishydrolysisdigestion
NCRH
COOH
H
H
2
N
CRHCCO
H
2
O
+
C
dipeptide
B
peptide bondR = rest of the moleculeor the side chain
A
More amino acids can attach by condensation onto the amine group at Band the acid group at C so that a long chain of amino acids (a polypeptide)can be assembled. Polypeptides may be folded and cross-bonded intoparticular three dimensional shapes and assembled together into proteins.This involves
hydrogen
and
sulphur
bonds (described below) rather thanpeptide bonds.
Ionic attractions
may also be important in stabilising thethree dimensional shapes of proteins. This is illustrated in Fig 5.
Fig 5. Ionic association (attraction) between two parts of apolypeptide chain.
COO
-
NH
2+
polypeptide chainattraction betweenionised acid amine groups
Formation of ester bonds in lipid structure
An ester bond is formed by condensation between an acid and an alcohol.The main alcohol involved in lipid structure is glycerol (which has 3 alcoholor –OH groups) and the acids involved are fatty acids. Fig 6 shows theformation of a triglyceride.
Fig 6. Formation of a triglyceride
CH
2
OH + HOOC.RCHOH + HOOC.RCH
2
OH + HOOC.RCH
2
O C.RCHO C.RCH
2
O C.R+ 3H
2
O
hydrolysis/ digestioncondensation/ synthesis
ester bondtriglyceridewaterglycerolfatty acidsR = rest of the molecule or the side chainOOO
 
Bio Factsheet
3
Hydrogen bonding
Water consists of two hydrogen atoms, each of which shares an electronwith the single oxygen atom. These shared electrons (negative) lie closer tothe oxygen than to the hydrogens (positive protons) and so the moleculebecomes a charged dipole, with two partial positive charges at one end anda partial negative charge at the other end. This is shown in Fig 7.
Fig 7 . The water molecule
Because of these charges the hydrogen atoms of one water molecule areattracted to the oxygen atoms of adjacent water molecules. These attractionsare called hydrogen bonds and are shown in Fig 8.
Fig 8. Hydrogen bonding between water molecules.
O
 .  .
HH104.5
o
δ
+
δ
+
δ
-
shared electronpairspartial charges
Chemical bonding in biological molecules
OHHOHHOHHOHHOHHhydrogen bonding
 
Hydrogen bonds occur between:parallel cellulose molecules holding them together in fibrils,opposite purine and pyrimidine bases holding DNA structure togetherpolypeptide chains holding shape and protein structure together.Fig 9 shows hydrogen bonds between nearby peptide bonds between twopolypeptides.
Fig 9. Hydrogen bonding in polypeptidesSulphur bonds
Amino acids such as cysteine and methionine contain sulphydryl (-SH)groups. The group has reducing properties since the H atom can be fairlyeasily removed. In proteins two nearby –SH groups may become oxidised(hydrogen lossed) forming a cross-linking sulphur bond (–S-S-).Sulphur bonds are stronger and more heat stable than hydrogen bonds andso proteins that contain many sulphur bonds tend to have good stability.The RNA splitting enzyme, ribonuclease, for example, does not denature(break down) unless temperatures are raised to around 95
o
C whereas mostproteins denature above 42
o
C.
Phosphate bonds
These are found joining the adjacent nucleotides in DNA and RNAstructure. They are formed by condensations of orthophosphoric acid(H
3
PO
4
) between the –OH groups on carbon 3 of one pentose sugar andcarbon 5 of the pentose sugar of the next nucleotide. This is illustrated inFig 10.
Fig 10. Orthophosphoric acid and a phosphate bond in RNA
CC
C
COOHOHHOHCH
2
O - baseHOH
2
CPOHOPOHOCCCCOOHOHHOHCH
2
O - baseHOH
2
C
POHOPOHOOHOHorthophosphoricacidphosphate bondribose sugar
carbon 3carbon 5RNA
Exam Hint 
– Although examiners will not expect you to be able to write down structural formulae from memory, you will be expected to recognise molecular structures and to be able to manipulate moleculeby joining them together with appropriate bonding.
CNCNCCRHOHRHOHCONHCRHCOHNNHCCNCNHOHORCONHCOHCHRCHRpeptide bond
δ
+
δ
+
δ
-
δ
-
The dotted lines represent hydrogen bondspolypeptide chains111partial charges attract

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