Download Molecules of Life

Molecules
of Life
Tina Šantl-Temkiv
Department of Bioscience
Department of Physics and Astronomy
Aarhus University
Building blocks of life
Polymers=
Macromolecules
Elements &
monomers
Structures &
organisms
The essential elements
of life
1000000
Mass fraction [ppm]
100000
10000
1000
100
10
1
C – the backbone of organic
compounds
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
Chains of life
Polymerization: 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
CHEMICAL REACTIONS
• Hydrological cycle dilutes compounds in water bodies on Earth
• Membranes (=cell enclosures) keep molecules together at relatively
high concentrations
• Retain water in desiccating conditions
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)
Lipids
Fatty acids and triglycerides:
- energy storing molecules of life
Phospholipids (amphiphilic molecules)
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
Transcription
DNA
replication
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
Transcription
DNA
replication
Translation
Sugar-phosphate backbone in DNA
Pentose sugar (deoxyribose)
Phosphate
Deoxyribonucleic acid
Backbone:
• Holds the DNA molecule
together
• Mediates interaction with
other molecules
Nucleobases and nucleotides
NUCLEOBASES
Purines
Pyrimidines
NUCLEOTIDE – building
block of DNA
(Deoxyadenosine
monophosphate)
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 replication
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
The information storage system of life: controls
cell’s biochemistry
Central dogma of molecular biology:
unidirectional flow of sequence information between
information-carrying biopolymers
Transcription
DNA
replication
Translation
Ribonucleic acid
Transcription:
DNA to RNA
•
•
•
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
Transcription
DNA
replication
Translation
Carboxyl
Amino
> 500 amino
acids known
Carbon molecules made
from an amine and
carboxylic acid attached
to a central (alpha)
carbon
Essential amino acids
Proteins polymers of
amino acids
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.
H-bonds –> secondary
structure (3D)
Hairpins, helixes…
Tertiary and quarterly
structure
• Disulfide covalent bonds
form between cysteines
and methionines.
• Charged AA form ionic
bonds
Translation: RNA to proteins
tRNA
Carried different
AA
Anticodon at the
other end
Large subunit:
2 ribosomal RNA
(rRNA)
31 proteins
Small subunit:
1 ribosomal RNA (rRNA)
21 proteins
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.
Protein folding
A physical process resulting in the
native 3-dimensional structure of a
protein –> a biologically functional
conformation
Hydrophobic effect: hydrophobic chains
of a protein collapse into the core of the
protein
Chaperons: a class of proteins that aid the
correct folding of other proteins in vivo
Multimeric structure
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 compound
Structural components of
plant cell walls
Energy storage compound
Building blocks of life
Polymers=
Macromolecules
Elements &
monomers
Structures &
organisms
Building blocks of life
Polymers=
Macromolecules
Elements &
monomers
Structures &
organisms