Proteins - Département de Biologie

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Proteins - Département de Biologie
1.0 Organisation of the course « Introduction to biology »
Faculty
•  Patrick Charnay
•  Morgane Thomas-Chollier
•  Régis Ferrière
Students
Course and tutorials
Reference book
• Savada et al. (2010). Life. Sinauer associates
Home work (Charnay + Thomas-Chollier)
• Every week, in tutorials, presentation of an important point of the previous course in 5 min by two groups of two students (20% of the final note)
Evaluation (Charnay + Thomas-Cholier)
• Oral (30 min) for mathematicians, discussion on the course
• Written for chemists (course + exercises)
1.0 Organisation of the course « Introduction to biology »
1.0 Organisation of the course « Introduction to biology »
•  1 General introduction-Proteins
•  2 Carbohydrates, Lipids and Nucleic Acids
•  3 Cells
•  4 Metabolism and Cell Cycle
•  5 Organisms in their environment
•  6 Populations, communities, ecosystems
•  7 Inheritance and DNA
•  8 Gene Expression and Mutation
•  9 Regulation, Genomes and Recombinant DNA
•  10 Introduction to Development
•  11 Introduction to Evolution
•  12 Adaptation
1.1 General introduction
•  Related Sadava’s chapters:
1)  Studying life
2) Small Molecules and the Chemistry of Life
3) Proteins, Carbohydrates, and Lipids
1.2 What is Biology?
Characteristics of living organisms:
•  Consist of one or more cells
•  Contain genetic information
•  Use genetic information to reproduce
themselves
•  Are genetically related and have evolved
•  Can extract energy from the environment
1.2 What is Biology?
Evolution: a central theme of biology
• Living systems evolve through differential
survival and reproduction
• The processes of evolution have generated
the enormous diversity of life on Earth
1.2 What is Biology?
entérobactérie
diatomée
tardigrade
1 µm
10 µm
insecte
100 µm
champignon
oiseau
"reptile"
1 cm
BMC 12-13
1.2 What is Biology?
• Unicellular organisms: a single cell
carries out all the functions of life
• Multicellular organisms: made of many
cells that are specialized for different
functions
1.2 What is Biology?
• The study of cells was made possible by
the invention of microscopes.
• Robert Hooke in the 1600s described
repeating units of plant material as cells.
1.2 What is Biology?
Cell Theory: Matthias Schleiden and
Theodore Schwann (1838)
•  Cells are the basic structural and physiological units of all living
organisms.
•  Cells are both distinct entities and building blocks of more
complex organisms.
•  All cells come from preexisting cells
•  All cells are similar in chemical composition
•  Most of the chemical reactions of life occur within cells
•  Complete sets of genetic information are replicated and passed
on during cell division
1.2 What is Biology?
1.2 What is Biology?
• Evolution: change in the genetic
makeup of biological populations
through time
• Charles Darwin proposed that all living
organisms are descended from a
common ancestor by the mechanism of
natural selection
• Species: a group of organisms that can
produce viable and fertile offspring with
one another
1.2 What is Biology?
• Humans select for desired traits when
breeding animals
• Darwin postulated that natural selection
could occur through differential survival
and reproductive success
1.2 What is Biology?
• Genome: sum of all the DNA in a cell
• DNA: the information that is passed
from parent to daughter cells
• All cells in a multicellular organism have
the same genome
1.2 What is Biology?
• DNA consists of repeating subunits
called nucleotides
• Gene: a specific segment of DNA that
contains information for making a
protein
• Mutations are alterations in the
nucleotide sequence
1.2 What is Biology?
1.2 What is Biology?
• Metabolism: the sum total of all
chemical transformations and other
work done in all the cells of an organism
• The reactions are integrally linked – the
products of one are the raw materials of
the next
1.2 What is Biology?
• Multicellular organisms have an internal
environment that is not cellular
• Their cells are specialized or
differentiated, and organized into
tissues; tissues are organized into
organs
• Organ systems are groups of organs
with interrelated functions
1.2 What is Biology?
1.2 What is Biology?
• Model systems: using one type of
organism to understand others
• This is possible because all life is
related by descent from a common
ancestor, shares a genetic code, and
consists of similar building blocks: cells
1.2 What is Biology?
• Earth formed 4.6 to 4.5 billion years ago
but it was 600 million years or more
before life evolved
• The history of Earth can be pictured as
a 30-day month
1.2 What is Biology?
1.2 What is Biology?
• For 2 billion years, life consisted of
single cells called prokaryotes.
• These cells were in the oceans,
protected from UV radiation.
• There was little or no oxygen (O2) in the
atmosphere, and hence no protective
ozone (O3) layer.
1.2 What is Biology?
cellule procaryote typique
flagelle
membrane
cellulaire
cytoplasme
nucleoide
paroi
pili
~ 1 µm
Campbell & Reece
BMC 12-13
1.2 What is Biology?
Consequences of photosynthesis:
• O2 accumulated in the atmosphere
• Aerobic metabolism began
• Ozone layer formed, which allowed
organisms to live on land
1.2 What is Biology?
• Eukaryotic cells evolved from
prokaryotes
• These cells have intracellular
compartments called organelles with
specialized cellular functions
• The nucleus contains the genetic
information
1.2 What is Biology?
cellule eucaryote typique
noyau
reticulum endoplasmique
rugueux
centrosome
reticulum endoplasmique
lisse
vesicules
cis-Golgi
cytosol
trans-Golgi
mitochondrie
lysosome
~ 10-50 µm
endosome
trans-Golgi network
membrane cellulaire
matrice extracellulaire
BMC 12-13
1.2 What is Biology?
1.2 What is Biology?
La biologie*, une science récente
Les disciplines à l’intérieur de la biologie (XIXe et
XXe siècles) étaient traditionnellement définies par
leurs objets, ou le niveau de leur analyse, ou leurs
méthodes, ou leur échelle de temps
caractéristique ...
exemples: biochimie, génétique, biologie cellulaire,
physiologie, écologie, botanique, zoologie,
microbiologie, évolution (incluant la génétique des
populations)
et des sous-disciplines plus spécialisées:
immunologie, neurosciences ...
Lamarck (1744-1829)
ces sous-disciplines sont désormais beaucoup mieux intégrées (depuis moins de
trente ans)
* Jean-Baptiste de Lamarck (1802) "Recherches sur l’organisation des êtres vivants"
BMC 12-13
1.2 What is Biology?
Biologists use many methods to expand
our understanding of life.
• Observation: improved by new
technologies
• Experimentation
1.2 What is Biology?
1.2 What is Biology?
• Biological knowledge allows advances
in human pursuits such as medicine and
agriculture
• These advancements can raise ethical
and policy questions
• Biological knowledge contributes to our
understanding of human influences on
our environment
• Biologists are called on to advise
governments making policy decisions
1.2 What is Biology?
Distinguishing science and nonscience:
• Scientific hypotheses must be testable,
and have the potential of being rejected
• Science depends on evidence that
comes from reproducible and
quantifiable observations
1.3 Small molecules and the chemistry of life
1.3 Small molecules and the chemistry of life
1.3 Small molecules and the chemistry of life
•  Polar molecules that form hydrogen bonds
with water are hydrophylic (“water-loving”)
•  Nonpolar molecules such as hydrocarbons
that interact with each other, but not with
water, are hydrophobic (“water-hating”)
•  Individual interactions are brief and weak, but
summed over a large molecule, can be
substantial
1.4 Proteins
1.4 Proteins
• Proteins: combinations of 20 amino acids
• Carbohydrates: sugar monomers
(monosaccharides) are linked to form
polysaccharides
• Nucleic acids: 4 kinds of nucleotide
monomers
• Lipids: noncovalent forces maintain
interactions between lipid monomers
1.4 Proteins
• Polypeptide chain: single,
unbranched chain of amino acids.
• The chains are folded into specific
three dimensional shapes defined
by the sequence of the amino
acids.
1.4 Proteins
Functions of proteins include:
•  Enzymes—catalytic proteins
•  Structural proteins provide physical stability and
movement.
•  Defensive proteins (e.g., antibodies)
•  Receptor proteins—receive and respond to molecular
signals
•  Transport proteins carry substances within the organism
(e.g., hemoglobin).
•  Genetic regulatory proteins regulate when, how, and to
what extent a gene is expressed.
1.4 Proteins
Amino acids have carboxyl and amino
groups—so they function as both acid
and base
1.4 Proteins
The peptide bond is inflexible—no rotation is possible.
1.4 Proteins
These hydrophylic amino acids attract ions of opposite
charges.
1.4 Proteins
Hydrophylic amino acids with polar, but uncharged side
chains form hydrogen bonds.
1.4 Proteins
1.4 Proteins
Hydrophobic amino acids
1.4 Proteins
• The primary structure of a protein is
the sequence of amino acids
• The sequence determines secondary
and tertiary structure—how the protein
is folded
• The number of different proteins that
can be made from 20 amino acids is
enormous!
1.4 Proteins
1.4 Proteins
Secondary structure:
• α helix—right-handed coil resulting
from hydrogen bonding between N—H
groups on one amino acid and C=O
groups on another
• β pleated sheet—two or more
polypeptide chains are aligned;
hydrogen bonds from between the
chains
1.4 Proteins
• Tertiary structure: Bending and folding
results in a macromolecule with specific
three-dimensional shape
• The outer surfaces present functional
groups that can interact with other
molecules
1.4 Proteins
Tertiary structure is determined by
interactions of R-groups:
• Disulfide bridges
• Hydrogen bonds
• Aggregation of hydrophobic side chains
• van der Waals forces
• Ionic bonds
1.4 Proteins
Complete descriptions of tertiary structure have been
worked out for many proteins (in this case Lysozyme)
1.4 Proteins
Proteins bind noncovalently with specific
molecules. The specificity is determined
by:
• Protein shape—there must be a general
“fit” between the 3-D shapes of the
protein and the other molecule
• Chemistry—R groups on the surface
interact with molecules via ionic bonds,
hydrophobically, or hydrogen bonds
1.4 Proteins
Quaternary structure results from the interaction of subunits by
hydrophobic interactions, van der Waals forces, ionic bonds, and
hydrogen bonds.
Each subunit has its own unique tertiary structure.
1.4 Proteins
1.4 Proteins
• If a protein is heated, the secondary and
tertiary structure is broken down; the
protein is said to be denatured
• When cooled, the protein may return to
normal tertiary structure, demonstrating
that the information to specify protein
shape is contained in its primary
structure
1.4 Proteins
Conditions that affect secondary and tertiary
structure:
• High temperature
• pH changes
• High concentrations of polar molecules
• Nonpolar substances
1.4 Proteins
Lectures utiles
Savada et al.
Life (9th, Freeman, 2009, ~1200p)
+ online material
Stryer
Biochemistry (4th, Freeman, 1995, ~1.000p)
Biochimie (4e, Flammarion, 1997)
Biochemistry (6th, with collaborators)
Alberts et al.
Molecular biology of the cell (5th, Garland, 2007)
Biol. moléc. de la cellule (4e, Flammarion, 2004, 1472p)
Brown
Genomes (3rd, Bios, 2006, ~700p)
Genomes (2e, Flammarion, 2004, 585p)
Gilbert
Developmental biology (9th, 2010, ~700p)
BMC 12-13