BI6101 L02 Building Blocks

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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

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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
http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.htmlhttp://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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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

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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.html

Documents

BI6101 L02 Building Blocks