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Biochem-700 3(3-0)
CONCEPTS OF BIOCHEMISTRY
Dr Saba Chaudhry
(PhD Biochemistry)
Macromolecules
 Monomers + functional groups
Four types of macromolecules of
interest to us:
 Carbohydrates
 Proteins
 Lipids
 Nucleic Acids
Carbohydrates
 Monomer: simple sugar
 eg. Glucose
 Functional group(s):
 Carbonyl
 Hydroxyl
 Polymer: complex
CHO
 Starch, glycogen
Structure of
monosaccharide
Fisher
projection
• The straight
chain
structural
formula
Haworth
projection
• Cyclic
formula or
ring
structure
X-ray
diffraction
analysis
• Boat and
chair form
A. MONOSACCHARIDES
•Aldoses
• monosaccharides
containing an aldehyde
group
Straight chain
Ring structure
Chair form
7
9
A. MONOSACCHARIDES
• Ketoses
• monosaccharides
containing a ketone
group
DISACCHARIDES
 These are glycosides formed by the condensation of 2
simple sugars.
 If the glycosidic linkage involves the carbonyl groups
of both sugars ( ) the resulting
disaccharide is
 On the other hand, if the glycosidic linkage involves
the carbonyl group of only one of the 2 sugars (as in
maltose and lactose) the resulting disaccharide is
reducing.
Reducing versus none
reducing sugar
POLYSACCHARIDES
 These are formed by the condensation of n molecules of
monosaccharides with the removal of n-1 molecules of water.
Since condensation involves the carbonyl groups of the sugars,
leaving only one free carbonyl group at the end of a big molecule,
polysaccharides are non-reducing.
 They are of 2 types:
1. Homopolysaccharides (e.g. Starch, Glycogen, cellulose).
2. Heteropolysaccharides (e.g. glycosaminoglycans, glycoproteins)
16
17
Aldehyde
group
H-C=O
Monosaccharides
Enantiomers
Mirror images
of each other
Disaccharides
sucrose = glucose +
fructose
Lactose = galactose +
glucose
Maltose= glucose +
glucose
Oligosaccharides Polysaccharides
Homo-
Starch, glycogen,
cellulose
Hetero-
GAGs
Epimers
Differ in
configuration
around one
specific
carbon atom
Isomers
Same
chemial
formula
Ketoses
Keto
group
C=O
Aldoses
glycolipids have an
important role in the
immune response.
Functions of Carbohydrates
➢ Carbohydrates are the most abundant organic molecules in
nature.
❖ Providea significant fraction of the dietarycalories for most
organisms
❖ Act as a storage form of energy in the body,
❖ serve as cell membrane components that mediate some forms of
intercellularcommunication.
❖ Carbohydrates also serve as a structural component of many
organisms, including the cell walls of bacteria, the exoskeleton of
many insects, and the fibrous cellulose of plants.
❖ Ribose and deoxyribose in nucleic acids; Galactose in lactose of
milk, in glycolipids, and in combination withprotein in glycoproteins
and proteoglycans.
❖ Diseases associated with carbohydrate metabolism include
diabetes mellitus, galactosemia, glycogen storage diseases, and
lactose intolerance
Proteins
 Monomer: amino
acids
 20 total, 9 to 10
essential
 Functional group(s):
 Carboxyl
 Amino
 Polymer
 Polypeptide
 Protein
Protein Structure
 The 20 amino acids are joined together by
peptide bonds.
 The linear sequence contains the
information necessary to generate a
protein molecule with a unique three-
dimensional shape.
 The complexity of protein structure is best
analyzed by considering the molecule in
terms of four organizational levels, namely,
primary, secondary, tertiary, and
quaternary
Primary structure
 The sequence of amino acids in a protein
 The AA sequence must be written from
the N-terminus to the C-terminus.
 Many genetic diseases result in proteins
with abnormal amino acid sequences,
(Sickle cell anemia, Glu replaced with
Val)
Peptide bond
 Peptide bonds are
responsible for
maintaining the
primary structure
 Linkage of many
amino acids
through peptide
bonds results in an
unbranched chain
called a
polypeptide
SECONDARY STRUCTURE OF
PROTEINS
 Regular arrangements of amino acids that are
located near to each other in the linear sequence.
 The R group has an impact on the likelihood of
secondary structure formation
 The α-helix, β-sheet, and β-bend (β-turn) are
examples of secondary structures
Tertiary Structure
 The configuration of all the atoms in the protein
chain:
 side chains
 prosthetic groups
 helical and pleated sheet regions
Tertiary Structure
 Protein folding attractions:
 1. Non covalent forces
 a. Inter and intrachain H bonding
 b. Hydrophobic interactions
 c. Electrostatic attractions (+ to - ionic attraction)
 d. Complex formation with metal ions
 e. Ion-dipole
 2. Covalent disulfide bridges
A protein domain is a conserved part of a given protein sequence
and(tertiary) structure that can evolve, function, and exist
independently of the rest of the protein chain
Tertiary interactions
 Quaternary structure is the result of non covalent interactions
between two or more protein chains.
 Oligomers are multisubunit proteins with all or some identical
subunits.
 The subunits are called protomers.
 two subunits are called dimers
 four subunits are called tetramers
Quaternary structure
3
0
Lipids
Lipids are bio-molecules that are:
• Hydrophobic in nature because of the high amountof
Hydrocarbons in their structure
• Relatively insoluble in waterbut readily soluble in non-
polar solvents such as Chloroform, Benzene and Ether
• Easily separatedfrom other biological materials by
extraction into organic solvents because of their
hydrophobic properties
• Examples of lipids:
• Fats, Oils, Steroids, Waxes, Fat-soluble Vitamins (Vitamins A, D, E
and K),
LIPIDS
31
 Monomer: Fatty
acid
 Functional group(s):
 Carboxyl
 Polymers: many –
depending on the
type of lipid
 Phospholipid
LIPIDS
3
3
What are fatty acids?
Aliphatic Carboxylic Acids containing
Long Hydrocarbon chains that may be
Saturatedor Unsaturated,
Fattyacid has both Hydrophobic and
Hydrophilic properties, thus
are Amphipathic in nature,
• Non-polar Hydrophobic Hydrocarbon
Chain (Tail)
• Polar (-COOH) group (Hydrophilic
Head)
Examples of fattyacids: Palmitic Acid,
Oleic Acid, Arachidonic Acid, Linoleic
Acid, Linolenic Acid, etc.
Nucleic Acids
Nucleic acids are:
• molecules that store information for cellular growth
and reproduction.
• deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA).
• large molecules consisting of long chains of
monomers called nucleotides.
34
Nucleic Acids
The nucleic acids DNA and RNA
consist of monomers called
nucleotides that consist of a
• pentose sugar.
• nitrogen-containing base.
• phosphate.
Nucleotide
Nitrogen Bases
The nitrogen bases in
DNA and RNA are
• pyrimidines C, T, and U.
• purines A and G.
36
Pentose Sugars
The pentose (five-carbon) sugar
• in RNA is ribose.
• in DNA is deoxyribose with no O atom on carbon 2’.
• has carbon atoms numbered withprimes to distinguish them
from the atoms in nitrogen bases.
37
Names of Nucleosides and
Nucleotides
38
Primary Structure of Nucleic
Acids
In the primary structure of nucleic acids
• nucleotides are joined by phosphodiester
bonds.
• the 3’-OH group of the sugar in one nucleotide
forms an ester bond to the phosphate group
on the 5’-carbon of the sugar of the next
nucleotide.
39
Primary Structure of Nucleic
Acids
40
Structure of Nucleic Acids
A nucleic acid
• has a free 5’-phosphate group
at one end and a free 3’-OH
group at the other end.
• is read from the free 5’-end
using the letters of the bases.
• This example reads
—A—C—G—T—.
41
Compaction
of DNA in a
eukaryotic
chromosome

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2. Macromolecule in Biochemistry.pdf

  • 1. Biochem-700 3(3-0) CONCEPTS OF BIOCHEMISTRY Dr Saba Chaudhry (PhD Biochemistry)
  • 2. Macromolecules  Monomers + functional groups Four types of macromolecules of interest to us:  Carbohydrates  Proteins  Lipids  Nucleic Acids
  • 3. Carbohydrates  Monomer: simple sugar  eg. Glucose  Functional group(s):  Carbonyl  Hydroxyl  Polymer: complex CHO  Starch, glycogen
  • 4. Structure of monosaccharide Fisher projection • The straight chain structural formula Haworth projection • Cyclic formula or ring structure X-ray diffraction analysis • Boat and chair form
  • 7. 7
  • 8.
  • 9. 9
  • 10. A. MONOSACCHARIDES • Ketoses • monosaccharides containing a ketone group
  • 11. DISACCHARIDES  These are glycosides formed by the condensation of 2 simple sugars.  If the glycosidic linkage involves the carbonyl groups of both sugars ( ) the resulting disaccharide is  On the other hand, if the glycosidic linkage involves the carbonyl group of only one of the 2 sugars (as in maltose and lactose) the resulting disaccharide is reducing.
  • 12.
  • 13.
  • 15. POLYSACCHARIDES  These are formed by the condensation of n molecules of monosaccharides with the removal of n-1 molecules of water. Since condensation involves the carbonyl groups of the sugars, leaving only one free carbonyl group at the end of a big molecule, polysaccharides are non-reducing.  They are of 2 types: 1. Homopolysaccharides (e.g. Starch, Glycogen, cellulose). 2. Heteropolysaccharides (e.g. glycosaminoglycans, glycoproteins)
  • 16. 16
  • 17. 17
  • 18.
  • 19. Aldehyde group H-C=O Monosaccharides Enantiomers Mirror images of each other Disaccharides sucrose = glucose + fructose Lactose = galactose + glucose Maltose= glucose + glucose Oligosaccharides Polysaccharides Homo- Starch, glycogen, cellulose Hetero- GAGs Epimers Differ in configuration around one specific carbon atom Isomers Same chemial formula Ketoses Keto group C=O Aldoses glycolipids have an important role in the immune response.
  • 20. Functions of Carbohydrates ➢ Carbohydrates are the most abundant organic molecules in nature. ❖ Providea significant fraction of the dietarycalories for most organisms ❖ Act as a storage form of energy in the body, ❖ serve as cell membrane components that mediate some forms of intercellularcommunication. ❖ Carbohydrates also serve as a structural component of many organisms, including the cell walls of bacteria, the exoskeleton of many insects, and the fibrous cellulose of plants. ❖ Ribose and deoxyribose in nucleic acids; Galactose in lactose of milk, in glycolipids, and in combination withprotein in glycoproteins and proteoglycans. ❖ Diseases associated with carbohydrate metabolism include diabetes mellitus, galactosemia, glycogen storage diseases, and lactose intolerance
  • 21. Proteins  Monomer: amino acids  20 total, 9 to 10 essential  Functional group(s):  Carboxyl  Amino  Polymer  Polypeptide  Protein
  • 22. Protein Structure  The 20 amino acids are joined together by peptide bonds.  The linear sequence contains the information necessary to generate a protein molecule with a unique three- dimensional shape.  The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels, namely, primary, secondary, tertiary, and quaternary
  • 23. Primary structure  The sequence of amino acids in a protein  The AA sequence must be written from the N-terminus to the C-terminus.  Many genetic diseases result in proteins with abnormal amino acid sequences, (Sickle cell anemia, Glu replaced with Val)
  • 24. Peptide bond  Peptide bonds are responsible for maintaining the primary structure  Linkage of many amino acids through peptide bonds results in an unbranched chain called a polypeptide
  • 25. SECONDARY STRUCTURE OF PROTEINS  Regular arrangements of amino acids that are located near to each other in the linear sequence.  The R group has an impact on the likelihood of secondary structure formation  The α-helix, β-sheet, and β-bend (β-turn) are examples of secondary structures
  • 26. Tertiary Structure  The configuration of all the atoms in the protein chain:  side chains  prosthetic groups  helical and pleated sheet regions
  • 27. Tertiary Structure  Protein folding attractions:  1. Non covalent forces  a. Inter and intrachain H bonding  b. Hydrophobic interactions  c. Electrostatic attractions (+ to - ionic attraction)  d. Complex formation with metal ions  e. Ion-dipole  2. Covalent disulfide bridges A protein domain is a conserved part of a given protein sequence and(tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain
  • 29.  Quaternary structure is the result of non covalent interactions between two or more protein chains.  Oligomers are multisubunit proteins with all or some identical subunits.  The subunits are called protomers.  two subunits are called dimers  four subunits are called tetramers Quaternary structure
  • 30. 3 0 Lipids Lipids are bio-molecules that are: • Hydrophobic in nature because of the high amountof Hydrocarbons in their structure • Relatively insoluble in waterbut readily soluble in non- polar solvents such as Chloroform, Benzene and Ether • Easily separatedfrom other biological materials by extraction into organic solvents because of their hydrophobic properties • Examples of lipids: • Fats, Oils, Steroids, Waxes, Fat-soluble Vitamins (Vitamins A, D, E and K), LIPIDS
  • 31. 31
  • 32.  Monomer: Fatty acid  Functional group(s):  Carboxyl  Polymers: many – depending on the type of lipid  Phospholipid LIPIDS
  • 33. 3 3 What are fatty acids? Aliphatic Carboxylic Acids containing Long Hydrocarbon chains that may be Saturatedor Unsaturated, Fattyacid has both Hydrophobic and Hydrophilic properties, thus are Amphipathic in nature, • Non-polar Hydrophobic Hydrocarbon Chain (Tail) • Polar (-COOH) group (Hydrophilic Head) Examples of fattyacids: Palmitic Acid, Oleic Acid, Arachidonic Acid, Linoleic Acid, Linolenic Acid, etc.
  • 34. Nucleic Acids Nucleic acids are: • molecules that store information for cellular growth and reproduction. • deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). • large molecules consisting of long chains of monomers called nucleotides. 34
  • 35. Nucleic Acids The nucleic acids DNA and RNA consist of monomers called nucleotides that consist of a • pentose sugar. • nitrogen-containing base. • phosphate. Nucleotide
  • 36. Nitrogen Bases The nitrogen bases in DNA and RNA are • pyrimidines C, T, and U. • purines A and G. 36
  • 37. Pentose Sugars The pentose (five-carbon) sugar • in RNA is ribose. • in DNA is deoxyribose with no O atom on carbon 2’. • has carbon atoms numbered withprimes to distinguish them from the atoms in nitrogen bases. 37
  • 38. Names of Nucleosides and Nucleotides 38
  • 39. Primary Structure of Nucleic Acids In the primary structure of nucleic acids • nucleotides are joined by phosphodiester bonds. • the 3’-OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5’-carbon of the sugar of the next nucleotide. 39
  • 40. Primary Structure of Nucleic Acids 40
  • 41. Structure of Nucleic Acids A nucleic acid • has a free 5’-phosphate group at one end and a free 3’-OH group at the other end. • is read from the free 5’-end using the letters of the bases. • This example reads —A—C—G—T—. 41
  • 42. Compaction of DNA in a eukaryotic chromosome