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BiochemistrySetting the Stage

BiochemistrySetting the Stage

Early History of Biochemistry

Elements in Biomolecules

Biological Macromolecules

Organelles, Cells and Organisms

Early History of Biochemistry

Elements in Biomolecules

Biological Macromolecules

Organelles, Cells and Organisms

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BiochemistryBiochemistry

““The chemistry of the living cell.”The chemistry of the living cell.”

Biochemistry can be divided into two levels of study:

ConformationalConformational - structure and three dimensional arrangements of biomolecules.

InformationalInformational - language for communication inside and between cells.

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Roots of modern biochemistryRoots of modern biochemistry

China - 4th century BCChina - 4th century BCMan was composed of 5 elements - water, fire, wood, metal and earth.

Galen - Greek physician (129-199 AD)Galen - Greek physician (129-199 AD)Recognized pharmacology as means to good health. Used plant & animal products.

Arabic study of biologyArabic study of biologyFlourished in 762 AD.

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Roots of modern biochemistryRoots of modern biochemistry

Europe - 11th century ADEurope - 11th century ADGreek and Arabic literature arrived.

Paracelsus (1493-1551 AD)Paracelsus (1493-1551 AD)Key figure in European science. Started the movement away from ancient medical doctrines.

Real strides in biological (and other sciences) in 17th and 18th centuries - using a more molecular approach.

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Roots of modern biochemistryRoots of modern biochemistry

First organic/biochemical synthesisFirst organic/biochemical synthesis

Friedrick Wohler - Synthesis of Urea, 1828.

NH3 + NCOH NCO- NH4+ H2N-C-NH2

cyanic ammonium urea acid cyanate

O ||

..

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Road to modern biochemistryRoad to modern biochemistry

Two separate approaches were taken.

One route can be traced though the physical sciences which stressed structural characterization - chemistry and physics.

Another path was followed by biologists. They tended to characterize living organisms and cells.

The paths converged in 1952 with the characterization of DNA - Watson & Crick.

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Road to modern biochemistryRoad to modern biochemistry

Cell nuclei

Cell theory

GeneticsDiscovery of DNA

Genetics of Drosophila

DNA function

Chemistry used to describe biology

Description of fermentation

Urea Synthesis

Crystallization of urease

Description of glycolysis

Description of citric acid cycle

DNA double helixX-Ray of protein crystals Genetic code

Restriction EnzymesRecombinant DNA

Catalytic RNAPolymerase chain reaction

Gene therapy

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1990

Electron Microscope

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Living matter contains C, H, O, N, S and P

Living matter contains C, H, O, N, S and P

Only 28 of the 100 elements occur naturally in living systems.

Macroelements.Macroelements. C, H, O, N, P and S account for 92% of all elements in biomolecules.

Essential trace elements.Essential trace elements. Ca, Mg, Fe, I, Zn, Cu, ... Required in relatively small amounts.

Trace elements that may be essential.Trace elements that may be essential. Some elements like As, Br and Mo may be important but we don’t have sufficient data.

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Elements in living systems.Elements in living systems.

H

Li

Na

Cs

Rb

K

TlHgAuHfLaBa PtIrOsReWTa

He

RnAtPoBiPb

Be

Mg

Sr

Ca

CdAgZrY PdRhRuTcMoNb

ZnCuTiSc NiCoFeMnCrV

In XeITeSbSn

Ga KrBrSeAsGe

Al ArClSPSi

B NeFONC

I A II A III A IV A V A VI A VIIA VIIIA

III B IVB V B VIB VIIB VIII B IB IIB

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2

3

4

5

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macronutrientstrace essentialtrace, possibly essential

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BiomoleculesBiomolecules

There is a great variety of compounds used by living systems. Some examples:

CarbohydratesCarbohydrates - energy, cell structure, molecular recognition.

LipidsLipids - energy, cell membranes, hormones.

VitaminsVitamins - assortment of compounds that play many roles, essential parts of other biomolecules.

Amino acidsAmino acids - building blocks of proteins.

Porphyrin ringsPorphyrin rings - species like heme and chlorophyll.

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HemeHeme

Porphyrin rings play significant roles in a wide range of biomolecules.

Heme has an Fe2+ at its center. It forms a complex with oxygen which is used to transport O2.

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Biological macromoleculesBiological macromolecules

These are the ‘polymers’ of living systems.

Nucleic acidsNucleic acids - information storage and transfer. Made of sugar, phosphate and nitrogen bases.

ProteinsProteins - transport, structure and regulation. Produced from amino acids.

PolysaccharidesPolysaccharides - structure, energy storage. Made from simple sugars.

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Organelles, cells and organisms.Organelles, cells and organisms.

In many cases, biochemicals tend to cluster together, forming increasing more complex structures.

Even the simplest of these clusters are still very large.

A point is then reached where it is considered a ‘living’ system.

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Supramolecular assembliesSupramolecular assemblies

Organized clusters of macromoleculesOrganized clusters of macromolecules• Cell membranes - lipid/protein• Chromatin - DNA/protein• Ribosomes - RNA/protein• Cytoskeleton - fibrous protein structure• Viruses - assemblages of a DNA or RNA

strand wrapped in a protein package

While important, none of these are considered as ‘living.’

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VirusVirus

Head

DNA

Body

Tail filament

Bacteriophage(Complex shape)

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Prokaryotic cellsProkaryotic cells

Simplest living systems.Simplest living systems.

• 1-10m in diameter.

• Cellular components are encapsulated in a cell membrane and rigid cell wall.

• Cell is filled with cytoplasm.

• No substructures beyond supramolecular assembles.

• Each has one chromosome.

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Prokaryotic cellsProkaryotic cells

Cell wall Cell membrane

Ribosome

Mesosome Nucleotide

PiliFlagella

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Eukaryotic cellsEukaryotic cells

More advanced type of cell. All ‘advanced’ lifeforms are of this type.

• Larger cells - 10-100m.• Presence of organelles - membrane

enclosed packages of organized macromolecules - nucleus, endoplasmic reticulum, mitochondria.

• Specialized organelles based on cell type. Example - Plant cells have chloroplasts and animal cells have lysosomes.

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Eukaryotic cellsEukaryotic cells

Golgicomplex

Nucleus

Mitochondria

Endoplasmic reticulum

Vesicle