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The Building Blocks of Life
The key chemical components ofbiological systems
BI6101 Introductory Biology
MSc Bioinformatics, AY2012/2013, July Semester
Lecture 2 - Timothy Tan
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Hierarchy of Life
atoms
molecules
macromolecules
cells
tissues
organs
organisms
populations
communitiesecosystems
organelles
Levels of Biological Organisation
The Building Blocks
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Life Support
The Prerequisites for Life to Exist
Liquid water (and its peculiar properties!)
Energy (heat)
Organic molecules
contain Carbon, Hydrogen and Oxygen atoms
Other factors that support life
pH (acid, neutral, alkaline)
salinity (concentration of various ions/salts) temperature
redox conditions (reduction-oxidation)
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Chemistry of Life
Types of atomic bonds important for life
Covalent
eg. -CH- or -C=O-
Ionic/Polar eg. Na+ Cl-
Hydrogen bonds
eg. -HO H-
Hydrophobic interactions
eg. quaternary protein structure
van der Waals forces
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Organic Molecules
Carbon-based molecules
Backbone of Carbon atoms -C-C-C-C-C-C-
Functional groups containing C, H, O, N, P, S
Can be Linear or Ring structure
Varki & Sharon,Essentials of Glycobiology
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Can have isomers,chirality
OrganicMolecules Can form polymers
multiple monomer units condense together
monomers in chain referred to as residues
monomer
residue covalent bonds
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http://universe-review.ca/I15-32-chirality.jpg
OrganicMolecules
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Have Functional groups (R groups)
Attached to carbon backbone
Give molecules different properties
Group Symbol Properties
Methyl -CH3 Nonpolar
Hydroxyl -OH Polar
Carbonyl -C=O Polar
Amino -NH2 or -NH3+ Basic
Carboxyl -COOH or -COO- Acid
Phosphate -PO42- Acid
Sulfhydryl -SH Polar
OrganicMolecules
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Molecular Building Blocks
Nucleic Acids
Proteins
Lipids (Fats)
Carbohydrates (Sugars)
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Macromolecules
Living material is built from combinations ofthe molecular building blocks
Macro = large (complex)
http://www.accessexcellence.com/AB/GG/small_orgMols.html
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Proteins and nucleic acids Linear chain polymers
Carbohydrates
Linear and branching chain polymers (polysaccarides)
Macromolecules
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Covalent bonds are important in formingmacromolecules
Non-covalent bonds predominate in largerassemblies and interactions betweenmacromolecules
http://www.accessexcellence.com/AB/GG/mols_toScale.html
Macromolecules
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http://www.accessexcellence.com/AB/GG/macroMols.html
Macromolecules
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Nucleic Acids
Nucleic from the nucleus
Chemical basis of genetic material
DNA: Deoxyribonucleic Acid
RNA: Ribonucleic Acid
Nucleic acids consist oflong chains (polymers)of nucleotide monomers
Short chains sometimes called oligos(oligonucleotides)
Wikimedia Commons
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X-ray Crystallography
3D structure is calculated from diffraction pattern in
photographic image using Fourier Transformation
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Watson and Crick deduced thestructure of DNA from thediffraction pattern A double helix
Based on earlier work by Wilkinsand Franklin
Watson and Crick built the model ofDNA to demonstrate the
correctness of their predictions
(L-R): Francis Crick, J ames Watson, Maurice Wilkins, Rosalind Franklin
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Nucleotides
OH X
Phosphate group(s)
on 5 carbon
Hydroxyl group
on 3 carbon
Nitrogenous
base
5-carbon
sugar (Pentose)
If X is
OH : ribose
H: deoxyribose
123
45
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Base and Sugar together form a nucleoside
eg. adenine+ribose = adenosine
Nucleoside and phosphate(s) form a nucleotide eg. adenosine+phosphate = adenosine monophosphate
Add more phosphate groups = diphosphates andtriphosphates
Nucleotide monomer units (free nucleotides) are usuallythe nucleotide triphosphate form
When incorporated into nucleic acid chain, eachnucleotide residue is in the monophosphate form
C ?
Cytosine ?
Deoxycytidine ?
Deoxycytidylate triphosphate ?
Nucleotides
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Nucleosides & their mono-, di-, and triphosphates
Base Nucleoside Nucleotide Nucleotides
D
NA
A Adenine Deoxyadenosine Deoxyadenylate dAMP dADP dATP
GGuanine Deoxyguanosine Deoxyguanylate dGMP dGDP dGTP
C CytosineDeoxycytidine Deoxycytidylate dCMP dCDP dCTP
T Thymine Deoxythymidine Deoxythymidylate dTMP dTDP dTTP
RNA
A Adenine Adenosine Adenylate AMP ADP ATP
GGuanine Guanosine Guanylate GMP GDP GTP
C Cytosine Cytidine Cytidylate CMP CDP CTP
UUracilUridine Uridylate UMP UDP UTP
Nucleotides
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Formingthe Sugar
PhosphateBackbone
3 OH
Hydroxyl group
5 PO4
Phosphate
group
Phosphodiester
bond
Nucleotides
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Alberts et al.,Mol Biol of the Cell
Nucleotides
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Base Pairing
Chargaffs rules
Percentage of A = T, while C = G in all living things
Hydrogen Bonds form between
A = T
C G
known as base-pairing
Watson & Crick realised this gave the structure of DNAas well as a possible copying mechanism for thegenetic material
Nucleotides
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Two Hydrogen Bonds
Three Hydrogen Bonds
Nucleotides
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Nucleotides
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DNA Double Helix
Polymer of nucleotides Two strands in opposite
directions (5 3)
Base-pairing holds two strandstogether
Flexible, 2 nm wide
Helical twisting
Right-handed twist
Major Groove / Minor Groove
10 base-pairs per helical turn
Holds genetic information inthe s e q u e n c e of nucleotide
residues
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DNA vs RNA
DNA contains deoxyribose sugar
Usually exists as a double strand (dsDNA)
Carrier of genetic information in most living thingsand some viruses
Unwinds and splits into single strands (ssDNA) toreplicate or to read genetic code
Very stable polymer molecule
RNA contains ribose sugar Usually exists as a single strand (ssRNA)
Carrier of genetic information in RNA viruses
Unstable molecule that is easily destroyed
Thymine is replaced by Uracil
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Proteins
Most diverse group ofbiological macromolecules
Made up from 20 different kinds of amino acids
There are two other, very rare, amino acids
The sequence of amino acids in a protein is important
Sequence Structure Function
Have multiple roles in living organisms
Just about everything except encode geneticinformation
How final 3D structure forms is still not fully
understood
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Amino Acids
All amino acids (aa) have the same generalstructure Only the side-chain (R group) differs
Different side-chains confer different properties
i.e. R group defines an amino acid
C O-C
H
N
H O
+H
HR
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Am
inoacids
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http://web.mit.edu/esgbio/www/lm/proteins/aa/aminoacids.html
Am
inoacids
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Am
inoacids
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Polypeptides
Amino acids (aa) bond to form peptides
Short polymers of aa: oligopeptides
Long polymers of aa: polypeptides
The peptide bondCondensation reaction between amino and carboxyl
groups on two amino acid residues
Each polypeptide has an Amino terminal (-NH3+) has a Carboxyl terminal (-COO-)
will fold into a 3D shape, the exact shape of whichconfers its function (structure function)
one or more folded polypeptides = a protein
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C O-C
H
N
H O
+H
H
R
PeptideBond
C O-C
H
N
H O
R
H2O removed
C O-C
H
N
H O
R
C O-C
H
N
H O
R
Polypeptide carbon backbone
N C C N C C N C C
Amino
Terminal
(Basic)
Carboxyl
Terminal
(Acidic)
C O-C
H
N
H O
+H
HR
C O-C
H
N
H O
+H
HR
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Protein Structure
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Protein
Structure
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Unit of molecular weight: Dalton (Da)
Protein
Structure
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Lipids
Diverse groupof molecules
Non-polymeric
Hydrophobic / Non-polar Not soluble in water
Consists mostly of hydrocarbons
3 classes of Lipids Neutral Lipids (triglycerides / fats / oils)
Phospholipids
Steroids
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NeutralLipids
Triglycerides a.k.a. triacylglycerol
What fats and oils
are made of (not tobe confused with
body fat)
Glycerol molecule + 3 fatty acid side-chains
High-energy food storage
Building a Triglyceridehttp://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
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Fatty acids
Saturated (with hydrogen)-C-C-C-C-C-C-C-C-straight chain
Unsaturated-C-C-C=C-C-C=C-kinked
Type of fatty acid present inlipids influence their properties
Saturated (straighter) chainsallow closer packing denser
Hence, unsaturated fats aremore fluid at a giventemperature than saturatedfats
eg. margarine vs butter
Neu
tralLipids
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Phospholipid bilayer Core component of all
biological membranes
Self-assemble
Fluidity affected by type offatty acids present
Pho
spholipids
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Carbohydrates
Saccharides (Sugars; names have suffix ose) Contain C, H, O in ratio of 1:2:1
Carbon backbone: linear or circular
General formula of(CH2O)nwhere usually 3 n 8
eg. glucose (n=6), C6H12O6
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Polysaccharides
Polymer of saccharideresidues
Unbranched (Straight) vsBranched chains
Homopolymer vsHeteropolymer
Monomer: monosaccharide Dimer (two residues): disaccharide
Carb
ohydrates
Glycosidic bonds
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s
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Roles of Carbohydrates
Provide energy Metabolised to liberate energy eg. glucose
Building blocks to build complex carbohydrates
For structure eg. cellulose For storage of food/energy eg. glycogen, starch
Building block for other macromolecules eg. pentose sugar in nucleic acids
eg. conjugated with proteins glycoproteins
Inter-converted to other organic molecules eg. indirectly converted to fatty acids
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Carb
ohydrates
eg Glycogenhttp://www.wellesley.edu/Chemistry/chem227/sugars/oligo/glycogen.jpg
s
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eg. Glycogen
Polymer of glucose residues
Straight chains with branches every ~10 residues
Straight chain: (14) glycosidic bond
Branchpoint: (16) glycosidic bond
Highly-branched molecule
Space efficiency for storage
Multiple free ends for enzyme to digest
O
OH
CH2OH
OH
O
O
O
OH
CH2OH
OH
O
O
OH
CH2OH
OH
O
OH
CH2OH
OH
O
O
OH
CH2OH
OH
OO
O
OH
CH2
OH
O
O
OH
CH2OH
OH
O
O
OH
CH2OH
OH
14
6
23
5
HO
HO
Free ends
(16)
Branchpoint
(14) glycosidic bonds
Carb
ohydrates
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Other macromolecules
Combinationsof differentclasses oforganic molecules Form conjugates,
complexes, etc.
eg. Lipoproteins,glycoproteins, etc.
Riboproteins / ribozymes
Many key components of cellular machinery are complexes ofRNA and protein
Note: Other classes of organic and inorganic moleculesare also found in living things!
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Food, Glorious Food
Feeding/Eating provides energy and the materialto build biomass
Food consists of organic matter that is digested,breaking down complex macromolecules into its subunit
components eg. Proteins amino acids; Carbohydrates sugars
These simpler molecules are readily absorbed
Once absorbed, they could be processed
metabolised for energy
interconverted to other biomolecules building blocks for creation of complex macromolecules
Plants make carbohydrates from carbon dioxide,water and sunlight source of all food!
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Learning Resources
Chem1 Virtual Textbook: Chap 8b - Chemical Bondinghttp://www.chem1.com/acad/webtext/chembond/index.html
WikiBooks - AP Biology:The Chemical Building Blocks of Life
http://en.wikibooks.org/wiki/AP_Biology/The_Chemical_Building_Blocks_of_Life
Life The Science of Biology, 8th Ed., Chap 3:Macromolecules web tutorial/animationhttp://bcs.whfreeman.com/thelifewire8e/content/cat_010/0304001.html
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http://www.chem1.com/acad/webtext/chembond/index.htmlhttp://en.wikibooks.org/wiki/AP_Biology/The_Chemical_Building_Blocks_of_Lifehttp://en.wikibooks.org/wiki/AP_Biology/The_Chemical_Building_Blocks_of_Lifehttp://bcs.whfreeman.com/thelifewire8e/content/cat_010/0304001.htmlhttp://bcs.whfreeman.com/thelifewire8e/content/cat_010/0304001.htmlhttp://bcs.whfreeman.com/thelifewire8e/content/cat_010/0304001.htmlhttp://bcs.whfreeman.com/thelifewire8e/content/cat_010/0304001.htmlhttp://en.wikibooks.org/wiki/AP_Biology/The_Chemical_Building_Blocks_of_Lifehttp://en.wikibooks.org/wiki/AP_Biology/The_Chemical_Building_Blocks_of_Lifehttp://www.chem1.com/acad/webtext/chembond/index.htmlRecommended