BIOCHEMISTRY (I)

LIFS2210

Introduction of Biochemistry

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• Table of Contents
• Part I The Realm of Biochemistry
• Chapter 1 The Scope of Biochemistry
• Chapter 2 The Matrix of Life: Weak Interactions in an Aqueous Environment
• Chapter 3 The Energetics of Life
• Part II Molecular Architecture of Living Matter
• Chapter 4 Nucleic Acids
• Chapter 5 Introduction to Proteins: The Primary Level of Protein Structure
• Chapter 6 The Three-Dimensional Structure of Proteins
• Chapter 7 Protein Function and Evolution
• Chapter 8 Proteins in Motion: Contractile Systems and Molecular Motors
• Chapter 9 Carbohydrates: Sugars, Saccharides, Glycans
• Chapter 10 Lipids, Membranes, and Cellular Transportation
• Part III Dynamics of Life: Catalysis and Control of Biochemical Reactions
• Chapter 11 Enzymes: Biological Catalysts
• Chapter 12 Chemical Logic of Metabolism
• Part IV Dynamics of Life: Energy, Biosynthesis, and Utilization of Precursors
• Chapter 13 Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate
Pathway
• Chapter 14 Citric Acid Cycle and Glyoxylate Cycle
• Chapter 15 Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism
• Chapter 16 Photosynthesis
• Chapter 17 Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins
• Chapter 18 Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates
• Chapter 19 Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids
• Chapter 20 Metabolism of Nitrogenous Compounds: Principles of Biosynthesis, Utilization, and Turnover
• Chapter 21 Metabolism of Nitrogenous Compounds: Amino Acids, Porphyrins, and Neurotransmitters
• Chapter 22 Nucleotide Metabolism
• Chapter 23 Mechanisms of Signal Transduction
• Part V Information
• Chapter 24 Genes, Genomes, and Chromosome
• Chapter 25 DNA Replication
• Chapter 26 DNA Restructuring: Repair, Recombination, Rearrangement, Amplification
• Chapter 27 Information Readout: Transcription and Post-transcriptional Processing
• Chapter 28 Information Decoding: Translation and Post-translational Protein Processing
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• Chapter 29 Regulation of Gene Expression
Review lecture notes
Course website - CELT ([Link]

Read book chapters

Work on exercise questions of the
books
• Text book
Biochemistry (4th edition) by Mathews, Van Holde and Ahern

• Reference books
• Biochemistry (7th edition) by Berg, Tymoczko and Stryer
• Lehninger Principles of Biochemistry (6th edition) by Nelson
and Cox
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 1. What is Biochemistry ?
• Biochemistry is the application of chemistry to the
study of biological processes at the cellular and
molecular level.

• It emerged as a distinct discipline around the

beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex

molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and

whole organism

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 Principles of Biochemistry
• Cells (basic structural units of living organisms) are highly
organized and constant source of energy is required to maintain
the ordered state.

• Living processes contain thousands of chemical pathways.

Precise regulation and integration of these pathways are
required to maintain life

• Certain important pathways e.g. Glycolysis is found in almost all

organisms.

• All organisms use the same type of molecules: carbohydrates,

proteins, lipids & nucleic acids.

• Instructions for growth, reproduction and developments for

each organism is encoded in their DNA

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How does biochemistry impact you?

• Medicine

• Agriculture

• Industrial applications

• Environmental applications

• etc 6
 2. Molecular organization of Life
• elements
• simple organic compounds (monomers)
• macromolecules (polymers)
• supramolecular structures
• organelles
• cells
• tissues
• organisms

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 Range of the
sizes of objects
studies by
Biochemist and
Biologist

1 angstrom = 0.1 nm

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 The Cell is the Basic Unit of Life

E. coli cell Eukaryotic cells

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 Many Important Biomolecules are Polymers

lipids proteins carbo nucleic acids

monomer fatty acid amino acid glucose nucleotide

polymer phospholipid protein subunit cellulose DNA

supramolecular
membrane protein complex cell wall chromosome
structure

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 A. Proteins

• Proteins are composed of 20 common amino acids

• Each amino acid contains:
(1) Carboxylate group (-COO-)
(2) Amino group (-NH2)
(3) Side chain (R) unique to each amino acid

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 Proteins

monomer amino acid

polymer protein subunit

supramolecular
structure Enzyme complex

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 B. Polysaccharides

• Carbohydrates, or saccharides, are

composed primarily of C,H and O

• Polysaccharides are composed of saccharide

monomers

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 Carbohydrates

monomer glucose

polymer cellulose

supramolecular
structure cell wall

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 C. Nucleic Acids

• Polynucleotides
- nucleic acid
biopolymers are
composed of
nucleotide
monomers

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 Nucleic Acids

monomer nucleotide

polymer DNA

supramolecular
chromatin
structure

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 D. Lipids and Membranes

• Lipids are rich in carbon and hydrogen, but

contain little oxygen
• Lipids are not soluble in water
• Fatty acids are the simplest lipids: long chain
hydrocarbons, a carboxylate group at one end
• Fatty acids are often components of
glycerophospholipids

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 Lipids

monomer fatty acid

polymer phospholipid

supramolecular
membrane
structure

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 Biomolecules – Structure
Anabolic

• Building block • Macromolecule

• Simple sugar • Polysaccharide
• Amino acid • Protein (peptide)
• Nucleotide • RNA or DNA
• Fatty acid • Lipid

Catabolic

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Common theme:

Monomers form
polymers through
condensations

Polymers are broken

down through
hydrolysis.

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 3. Water
•About 60-90 percent
of an organism is water

Water is used in
most reactions in
the body
Water is called
the universal
solvent
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 Hydrogen Bonding in Water

• Water molecules attract each other due to their

polarity
• A hydrogen bond is formed when a partially
positive hydrogen atom attracts the partially
negative oxygen atom of a second water molecule
• Hydrogen bonds can form between
electronegative atoms and a hydrogen attached to
another electronegative atom
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 Ionic and Polar Substances
Dissolve in Water

• Hydrophilic (water-loving) substances (polar

and ionic (electrolytes)) readily dissolve in H2O

• Polar water molecules align themselves around

ions or other polar molecules

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 Nonpolar Substances Are
Insoluble in Water

• Hydrophobic (water-fearing) molecules are

nonpolar
• Hydrophobic effect - the exclusion of nonpolar
substances by water (critical for protein folding
and self-assembly of biological membranes)
• Amphipathic molecules have hydrophobic
chains and ionic or polar ends. Detergents
(surfactants) are examples.
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 4. Noncovalent Interactions in
Biomolecules

Weak noncovalent interactions are important in:

• Stabilization of proteins and nucleic acids
• Recognition of one biopolymer by another
• Binding of reactants to enzymes

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 Noncovalent forces

There are four major types of noncovalent forces:

(1) Charge-charge interactions
(2) Hydrogen bonds
(3) Van der Waals forces
(4) Hydrophobic interactions

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A. Charge-Charge Interactions (Ion Pairing)

• Electrostatic interactions between two charged

particles
• Can be the strongest type of noncovalent forces
• Can extend over greater distances than other
forces
• Charge repulsion occurs between similarly
charged groups

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 B. Hydrogen Bonds

• Among the strongest of noncovalent interactions

• H atom bonded to N, O, S can hydrogen bond to
another electronegative atom (~0.2 nm distance)
• Total distance between the two electronegative
atoms is ~0.27 to 0.30 nm
• In aqueous solution, water can H-bond to exposed
functional groups on biological molecules

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 C. Van der Waals Forces

• Weak short range forces between:

(a) Permanent dipoles of two uncharged molecules
(b) Permanent dipole and an induced dipole in a
neighboring molecule
• Occurs when outer electron orbitals overlap
• Although individually weak, many van der Waals
interactions occur in biological macromolecules and
participate in stabilizing molecular structures

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 D. Hydrophobic Interactions

• The interactions between nonpolar molecules and

water are not as favorable as are interactions
between water molecules themselves

• Water molecules form “cages” around the nonpolar

molecules

• As two such nonpolar molecules come together,

some of the water molecules are released, and so
they can interact freely with bulk water

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Hydrophobic effect

Water H2O

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 The Chemical Elements of Life

• Only six nonmetallic elements: oxygen, carbon,

hydrogen, nitrogen, phosphorous, and sulfur
account for >97% of the weight of most organisms
• These elements can form stable covalent bonds
• Water is a major component of cells
• Carbon is more abundant in living organisms than
it is in the rest of the universe

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