molecules of lifehotmol.eu/pdf/3_b1_molecules_of_life_tsantl-temkiv.pdfcarbon molecules made from an...
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Molecules of Life
Tina Šantl-Temkiv
Department of BioscienceDepartment of Physics and AstronomyAarhus University
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Building blocks of life
Elements & monomers
Polymers=Macromolecules
Structures & organisms
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The essential elements of life
1
10
100
1000
10000
100000
1000000
Mas
s fr
acti
on
[p
pm
]
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Great diversity of possible compounds:
• Forms stable bonds with important elements: H, N, O, P, S
• The bonds can also be broken down, to make metabolisms possible
• The energy of different bonds, e.g. C-H (413 kJ/mol) and C-O (360 kJ/mol), is comparable to a C-C (347 kJ/mol)
–> easy interchange between these bonds
• Stable C=C and C≡C bonds
C – the backbone of organic compounds
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Chains of lifePolymerization: single molecules are covalently bound together into chains
Self-assembly: • intramolecular self-assembly (folding)
• intermolecular self-assembly - noncovalent interactions (hydrogen bonding, hydrophobic forces, van der Waals forces…)
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Water: life requires a solvent • All macromolecules assembly and biochemical
reactions must take place in a liquid environment.
• Viscosity and density of a solvent must allow molecules:• at sufficient concentrations• moving around rapidly enough for chemical reactions to
occur.
• Characteristics of water:• Dipole moment –> dissolves salts and small organic
molecules• Hydrogen bonding –> wide temperature range of liquid water• Ice has a lower density than water
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Membranes
• Hydrological cycle dilutes compounds in water bodies on Earth
• Membranes (=cell enclosures) keep molecules together at relatively high concentrations
• Retain water in desiccating conditions
CH
EMIC
AL
REA
CTI
ON
S
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Lipids
A wide diversity of chained an ring-containing compounds
Long chained carboxylic acids (fatty acids)
Cholesterol in animal cell membranes=> fluidity and integrity (change shape and move)
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LipidsPhospholipids (amphiphilic molecules)
Fatty acids and triglycerides:- energy storing molecules of life
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Lipids: phospholipids (amphiphilic molecules)
Lipid monolayers and bilayers form through self-assembly in water (hydrophobic interactions).Spontaneous and common process –fatty acids extracted from meteorites
In cells lipid bilayer – a complex system containing proteins and carbohydrates. Regulation of internal environment and its communication to the exterior.
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Selective permeability –Membrane potential
• Passive diffusion of small electrically neutral molecules
• Polar molecules (AA, nucleic acids, ions…) cannot diffuse
• Cell control the movement of these polar molecules via transmembrane protein complexes
• Concentration gradients across the membrane
• Negative voltage in the cell interior as compared to the cell exterior => a battery: provides power to operate cellular functions
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ATP synthases
• Energy: hydrogen ions (H+) moving down an electrochemical gradient
• Chemical energy in the form of adenosine triphosphate (ATP) molecule, a common "energy currency" of cells
• Reversible: Large-enough quantities of ATP cause it to create a transmembrane proton gradient
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The information storage system of life: controls cell’s biochemistry
Central dogma of molecular biology:
unidirectional flow of sequence information between information-carrying biopolymers
DNA replication
Transcription Translation
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The information storage system of life: controls cell’s biochemistry
Central dogma of molecular biology:
unidirectional flow of sequence information between information-carrying biopolymers
DNA replication
Transcription Translation
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Sugar-phosphate backbone in DNA
Pentose sugar (deoxyribose) Phosphate
Backbone:• Holds the DNA molecule
together• Mediates interaction with
other molecules
Deoxyribonucleic acid
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Nucleobases and nucleotides
Purines
Pyrimidines
NUCLEOTIDE – building block of DNA(Deoxyadenosine monophosphate)
NUCLEOBASES
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Nucleic acids: the genetic code of DNA
Hydrogen bonding between nucleobases
Two antiparallel strands of bound by H-bonds in their centre
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Cell reproduction by mitosis/binary fission
DNA is replicated => two cells with exactly the same genetic information
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DNA-binding enzymes:• Helicase – enzyme that
separates the two strands by unzipping H-bonds
• DNA polymerase – enzyme that synthesizes the new DNA strands
Origin of replication – replication fork
DNA replication
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The information storage system of life: controls cell’s biochemistry
Central dogma of molecular biology:
unidirectional flow of sequence information between information-carrying biopolymers
DNA replication
Transcription Translation
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Transcription: DNA to RNA
Ribonucleic acid
• DNA is used as a template for a similar molecule
• RNA has the same fundamental structure as DNA
• Generally more reactive than DNA
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Transcription: DNA to RNA
• Promoter – sequence in DNA that is initial binding site for RNA polymerase
• Initiates transcription of a particular gene
• RNA polymerase reads along the DNA strand and generates messenger RNA (mRNA)
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The information storage system of life: controls cell’s biochemistry
Central dogma of molecular biology:
unidirectional flow of sequence information between information-carrying biopolymers
DNA replication
Transcription Translation
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Proteins polymers of amino acids
CarboxylAmino
> 500 amino acids known
Esse
nti
al a
min
o a
cid
s
Carbon molecules made from an amine and carboxylic acid attached to a central (alpha) carbon
Amino acids differ in side groups –> a vast variety of AA in nature
Only 20 AA commonly used in life. Different properties: polar, hydrophobic, charged
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Proteins: peptide and other bonds
Primary structure• Dehydration reaction between
amino and carboxyl group• The process of polymerization
results in a long chain of amino acids.
Tertiary and quarterly structure• Disulfide covalent bonds
form between cysteines and methionines.
• Charged AA form ionic bonds
H-bonds –> secondary structure (3D)Hairpins, helixes…
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Translation: RNA to proteins
Small subunit: 1 ribosomal RNA (rRNA)21 proteins
Large subunit: 2 ribosomal RNA (rRNA)31 proteins
tRNACarried different AAAnticodon at the other end
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Genetic code
• Sequence of mRNA: codon with 3 positions
4 × 4 × 4 = 64 possible combinations
=>Degeneracy of the genetic code
• Universal to all life forms => common ancestor
• One dimensional information is transformed into a 3D structure of a chemically active molecule.
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A physical process resulting in the native 3-dimensional structure of a protein –> a biologically functional conformation
Protein folding
Multimeric structure
Hydrophobic effect: hydrophobic chainsof a protein collapse into the core of the protein
Chaperons: a class of proteins that aid the correct folding of other proteins in vivo
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Protein functions in cells
• Molecule transport• Energy transport molecules
• DNA replication, transcription, translation
• Catalyzing chemical reactions
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Carbohydrates - polysaccharides Structural support and energy molecules
• Hydrated carbon atoms with a general formula of (CH2O)x
• Chains of monosaccharides• Glycosidic bond = O-bridged links between
monosaccharides• Sugars can also bind through N-glycosidic
and S-glycosidic bonds => great variety of molecules
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Carbohydrates - polysaccharides
Energy storage compoundStructural components of plant cell walls
Energy storage compound
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Building blocks of life
Polymers=Macromolecules
Structures & organisms
Elements & monomers
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Elements & monomers
Polymers=Macromolecules
Structures & organismsBuilding blocks of life