Transcript Chemistry of Life - Bilkent University

Chemistry of Life
3.1 Life’s molecular diversity is based on the
properties of carbon
• A carbon atom forms four covalent bonds
– It can join with other carbon atoms to make chains or
rings
Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
• Carbon skeletons vary in many ways
Ethane
Propane
Carbon skeletons vary in length.
Butane
Isobutane
Skeletons may be unbranched or branched.
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
Cyclohexane
Benzene
Skeletons may be arranged in rings.
3.3 Cells make a huge number of large molecules from a
small set of small molecules
• Most of the large molecules in living things are
macromolecules called polymers
– Polymers are long chains of smaller molecular units
called monomers
– A huge number of different polymers can be made
from a small number of monomers
• Cells link monomers to form polymers by
dehydration synthesis
1
2
3
Short polymer
Unlinked monomer
Removal of
water molecule
1
2
3
Longer polymer
4
• Polymers are broken down to monomers by the
reverse process, hydrolysis
1
2
3
4
Addition of
water molecule
1
2
3
Coating of
capture strand
Macromolecules
• Carbohydrates (simple sugar)
• Lipids (fatty acids)
• Proteins (amino acids)
• Nucleic acids (nucleotides)
Carbohydrates
• have the general formula [CH2O]n where
n is a number between 3 and 6
• function in
– short-term energy storage (such as sugar);
– as intermediate-term energy storage (starch
for plants and glycogen for animals); and
– as structural components in cells (cellulose) in
the cell walls of plants and many protists),
and chitin in the exoskeleton of insects and
other arthropods.
• The monosaccharides glucose and fructose are
isomers
– They contain the same atoms but in different
arrangements
Glucose
Fructose
Carbohydrates
• Monosaccharides are
single
(mono=one)sugars
• ribose (C5H10O5)
• glucose (C6H12O6)
Carbohydrates
• formed when two
Monosaccharides are
chemically bonded
together
• Sucrose, a common
plant disaccharide is
composed of the
monosaccharides
glucose and fructose.
• Lactose, milk sugar,
is a disaccharide
composed of glucose
and the
monosaccharide
galactose.
Dehydration reaction
Synthesis and digestion of disaccharides
3.6 Connection: How sweet is sweet?
• Various types of molecules, including nonsugars, taste sweet because they bind to “sweet”
receptors on the tongue
Table 3.6
http://www.cancer.gov/cancertopics/factsheet/Risk/artificial-sweeteners
Sweets
Discovery
• Charles Zuker, a neuroscientist at Howard
Hughes Medical Institute, made a startling
announcement: All the sweet things in life
are perceived by two receptors.
• More than 30 receptors code for bitter taste
but only a single receptor devoted to sweet.
• Bitter there are many and many are toxic
• Sweet all tasty and good
http://www.discover.com/issues/aug-05/departments/chemistry-of-artificial-sweeteners/
G-coupled Receptor Family
G-coupled proteins
• a protein family of transmembrane receptors
that transduce an extracellular signal (ligand
binding) into an intracellular signal (G
protein activation).
http://upload.wikimedia.org/wikipedia/en/3/33/G-protein-coupled_receptor.png
http://en.wikipedia.org/wiki/G-protein_coupled_receptor
Receptor binding
• Sucralose, for instance, fits more snugly in
the receptor than sucrose, partly because its
chlorine atoms carry a stronger charge than
the oxygen atoms they replaced.
(Polysaccharide)
• are large molecules composed of
individual monosaccharide units.
• The formation of the ester bond by
condensation
• (the removal of water from a
molecule) allows the linking of
monosaccharides into disaccharides
and polysaccharides.
Carbohydrates
(Polysaccharide)
• Starch and glycogen are polysaccharides that
store sugar for later use
• Cellulose is a polysaccharide in plant cell walls
Starch granules in
potato tuber cells
Glycogen granules
in muscle tissue
Cellulose fibrils in
a plant cell wall
Cellulose
molecules
Figure 3.7
Glucose
monomer
STARCH
GLYCOGEN
CELLULOSE
Starch
• starch is a combination of two polymeric
carbohydrates (polysaccharides) called
amylose and amylopectin. They differ in the
glycosidic bonds they make in between
glucose molecules.
• Can humans digest starch?
• What enzyme is used to digest starch?
Glycogen
• Glycogen is a polysaccharide that is the
principal storage form of glucose (Glc) in
animal and human cells.
• Glycogen is found in the form of granules
in the cytosol in many cell types.
Glycogen
• Hepatocytes (liver cells) have the highest
concentration of it - up to 8%
• In the muscles, glycogen is found in a
much lower concentration (1% of the
muscle mass), but the total amount exceeds
that in liver.
• Glycogen plays an important role in the
glucose cycle.
Glucose cycle
• When glucose enters a cell it is rapidly
converted to glucose 6-phosphate, by
hexokinase. The glucose cycle can occur in
liver cells due to a liver specific enzyme
glucose-6-phosphatase, which catalyse the
dephosphorylation of glucose 6-phosphate
back to glucose.
Insulin
• http://en.wikipedia.org/wiki/Insulin
Glucagon
• http://en.wikipedia.org/wiki/Glucagon
Cellulose
• Plants make it except
tunicates (animals)
• Cellulose is synthesized in
higher plants by enzyme
complexes localized at the
cell membrane called
cellulose synthase
http://en.wikipedia.org/wiki/Cellulose
Lipid
• involved mainly with long-term energy
storage
• They are generally insoluble in polar
substances such as water.
• Secondary functions of lipids are as
structural components (as in the case of
phospholipids that are the major building
block in cell membranes) and as
"messengers" (hormones) that play roles
in communications within and between
cells.
Lipid
• Lipids are composed of three fatty
acids (usually) covalently bonded to
a 3-carbon glycerol.The fatty acids
are composed of CH2 units, and are
hydrophobic/not water soluble.
• Fats are lipids whose main function is energy
storage
– They are also called triglycerides
• A triglyceride molecule consists of one glycerol
molecule linked to three fatty acids
Fatty acid
Figure 3.8B
Structure of Fatty Acids
Saturated and unsaturated fatty acids
• The fatty acids of unsaturated fats (plant oils)
contain double bonds
– These prevent them from solidifying at room
temperature
• Saturated fats (lard) lack double bonds
– They are solid at room temperature
Figure 3.8C
Structure of Triacylglycerols
(Fats)
Synthesis of fat
Phospholipids
Structure of Phospholipids
Phosphatidylcholine
• Major component of lecithin, protective
sheats of the brain
Phosphatidylethanolamine
• Major component of cephalin; it is found
particularly in nervous tissue such as the
white matter of brain, nerves, neural tissue,
and in spinal cord.
• Major phospholipid of bacteria
Structure of Phospholipids
Sphingomyelin
• sphingomyelin is a major component of
myelin, the fatty insulation wrapped around
nerve cells by Schwann cells or
oligodendrocytes.
• Multiple Sclerosis is a disease characterized
by deterioration of the myelin sheath,
leading to impairment of nervous
conduction.
Structure of Glycolipids
Glycolipids
• Glycolipids are carbohydrate-attached lipids. Their role is
to provide energy and also serve as markers for cellular
recognition.
• Ganglioside is a compound composed of a
glycosphingolipid (ceramide and oligosaccharide) with one
or more sialic acids (AKA n-acetylneuraminic acid) linked
on the sugar chain. It is a component the cell plasma
membrane which modulates cell signal transduction
events. They have recently been found to be highly
important in immunology. Natural and semisynthetic
gangliosides are considered possible therapeutics for
neurodegenerative disorders.
3.9 Phospholipids, waxes, and steroids are
lipids with a variety of functions
• Phospholipids are a major component of cell
membranes
• Waxes form waterproof coatings
• Steroids
are often
hormones
Figure 3.9
Cholesterol in the
membrane
Cholesterol
• Cholesterol is a sterol (a combination
steroid and alcohol) and a lipid found in the
cell membranes of all body tissues, and
transported in the blood plasma of all
animals.
LDL and HDL
• When doctors talk to their patients about the
health concerns of cholesterol, they are
often referring to "bad cholesterol", or lowdensity lipoprotein (LDL). "Good
cholesterol" is high-density lipoprotein
(HDL); this denotes the way cholesterol is
bound in lipoproteins, the natural carrier
molecules of the body.
http://en.wikipedia.org/wiki/Low-density_lipoprotein
HDL and LDL
• High-density lipoproteins (HDL) form a class of
lipoproteins, varying somewhat in their size (8-11
nm in diameter) and contents, that carry
cholesterol from the body's tissues to the liver.
• Generally, LDL transports cholesterol and
triglycerides away from cells and tissues that
produce more than they use, towards cells and
tissues which are taking up cholesterol and
triglycerides.
Nucleic Acids
• composed of monomer units known as
nucleotides.
• The main functions of nucleotides are
information storage (DNA), protein
synthesis (RNA), energy transfers (ATP
and NAD), and signaling molecules (cAMP)
• Nucleotides consist of a sugar, a
nitrogenous base, and a phosphate.
A nucleotide
• The monomers of nucleic acids are nucleotides
– Each nucleotide is composed of a sugar, phosphate,
and nitrogenous base
Nitrogenous
base (A)
Phosphate
group
Figure 3.20A
Sugar
DNA
Polymerization of Nucleotides
(Phosphodiester bond)
RNA
Proteins
• They are very important in biological
systems as control and structural
elements.
• The building block of any protein is the
amino acid, which has an amino end
(NH2) and a carboxyl end (COOH).
• The R indicates the variable component
(R-group) of each amino acid.
• Each amino acid contains:
– an amino group
– a carboxyl group
– an R group, which distinguishes each of the 20
different amino acids
Figure 3.12A
Amino
group
Carboxyl (acid)
group
• Each amino acid has specific properties
Leucine (Leu)
HYDROPHOBIC
Figure 3.12B
Serine (Ser)
Cysteine (Cys)
HYDROPHILIC
3.13 Amino acids can be linked by peptide
bonds
• Cells link amino acids together by dehydration
synthesis
• The bonds between amino acid monomers are
called peptide bonds
Carboxyl
group
Amino
group
PEPTIDE
BOND
Dehydration
synthesis
Amino acid
Figure 3.13
Amino acid
Dipeptide
Amino acids are linked together by joining the amino end
of one molecule to the carboxyl end of another. Removal of
water allows formation of a type of covalent bond known
as a peptide bond.
Formation of a peptide bond between two amino acids by
the condensation (dehydration) of the amino end of one
amino acid and the acid end of the other amino acid.
Protein Structure
•
•
•
•
Primary
Secondary
Tertiary
Quaternary
Primary structure
• The primary structure of a protein is the
sequence of amino acids, which is
directly related to the sequence of
information in the RNA molecule.
• The primary structure is the sequence of
amino acids in a polypeptide.
Secondary Structure
• It is the tendency of the
polypeptide to coil or due to Hbonding between R-groups
Tertiary Structure
• It occurs due to bonding (or in
some cases repulsion) between Rgroups.
Quaternary structure
• formed from one or more
polypeptides.
3.15 A protein’s primary structure is
its amino acid sequence
Primary
structure
Amino acid
Secondary
structure
Hydrogen
bond
Pleated sheet
Alpha helix
Figure 3.15, 16
3.17 Tertiary structure is the overall
shape of a polypeptide
Tertiary
structure
Polypeptide
(single subunit
of transthyretin)
Quaternary
structure
Transthyretin, with four
identical polypeptide subunits
Figure 3.17, 18