Molecules of Life

Tina Šantl-Temkiv

Department of BioscienceDepartment of Physics and AstronomyAarhus University

Building blocks of life

Elements & monomers

Polymers=Macromolecules

Structures & organisms

The essential elements of life

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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

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…)

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

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

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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)

LipidsPhospholipids (amphiphilic molecules)

Fatty acids and triglycerides:- energy storing molecules of life

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.

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

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

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

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

Sugar-phosphate backbone in DNA

Pentose sugar (deoxyribose) Phosphate

Backbone:• Holds the DNA molecule

together• Mediates interaction with

other molecules

Deoxyribonucleic acid

Nucleobases and nucleotides

Purines

Pyrimidines

NUCLEOTIDE – building block of DNA(Deoxyadenosine monophosphate)

NUCLEOBASES

Nucleic acids: the genetic code of DNA

Hydrogen bonding between nucleobases

Two antiparallel strands of bound by H-bonds in their centre

Cell reproduction by mitosis/binary fission

DNA is replicated => two cells with exactly the same genetic information

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

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

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

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)

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

Proteins polymers of amino acids

CarboxylAmino

> 500 amino acids known

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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

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…

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

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.

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

Protein functions in cells

• Molecule transport• Energy transport molecules

• DNA replication, transcription, translation

• Catalyzing chemical reactions

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

Carbohydrates - polysaccharides

Energy storage compoundStructural components of plant cell walls

Energy storage compound

Building blocks of life

Polymers=Macromolecules

Structures & organisms

Elements & monomers

Elements & monomers

Polymers=Macromolecules

Structures & organismsBuilding blocks of life