Transcript Slide 1

General Biology (Bio107)
Chapter 3 – Carbon & The
Molecular Diversity of Life
Life is based on carbon
• Although cells are 70-95% water, the rest
consists mostly of carbon-based
compounds.
• Proteins, DNA, carbohydrates, and other
molecules that distinguish living matter from
inorganic material are all composed of
carbon atoms bonded to each other and to
atoms of other elements.
– These other elements commonly include
hydrogen (H), oxygen (O), nitrogen (N), sulfur
(S), and phosphorus (P).
Carbon & Biomass
“Carbon chemistry rules Life …”
“All forms of life on planet Earth and all molecules they
produce are based on the chemical element carbon ….”
6
C
12.01
Simplified Bohr Atomic Model of Carbon
-
-
+
+
++
++
+
-
+
Electron (6)
Proton (6)
Neutron (6,7 or 8)
-
• The study of carbon compounds, organic
chemistry, focuses on any compound
with carbon (organic compounds).
– While the name, organic compounds, implies
that these compounds can only come from
biological processes, they can be synthesized
by non-living reactions.
– Organic compounds can range from the
simple (CO2 or CH4) to complex molecules,
like proteins, that may weigh over 100,000
daltons.
• The science of organic chemistry began in
attempts to purify and improve the yield of products
from other organisms.
– Later chemists learned to synthesize simple
compounds in the laboratory, but they had no
success with more complex compounds.
– The Swedish chemist Jons J. Berzelius was
the first to make a distinction between organic
compounds that seemed to arise only in living
organisms and inorganic compounds from the
nonliving world.
• This lead early organic chemists to propose
vitalism, the belief in a life outside the limits of
physical and chemical laws.
• Support for vitalism began to wane as organic
chemists learned to synthesize more complex
organic compounds in the laboratory.
– In the early 1800’s the German chemist
Friedrich Wöhler was able to synthesize urea
from totally inorganic starting materials.
• In 1953, Stanley Miller at the
University of Chicago was able
to simulate chemical conditions
on the primitive Earth to
demonstrate the spontaneous
synthesis of organic compounds.
• Carbon atoms are the most versatile
building blocks of molecules.
• With a total of 6 electrons, a carbon atom
has 2 in the first shell and 4 in the second
shell.
– Carbon has little tendency to form ionic bonds
by loosing or gaining 4 electrons.
– Instead, carbon usually completes its valence
shell by sharing electrons with other atoms in
four covalent bonds.
– This tetravalence by carbon makes large,
complex molecules possible.
• When carbon forms covalent bonds with four
other atoms, they are stably arranged at the
corners of an imaginary tetrahedron structure
with bond angles near 109o.
– While drawn flat, they are actually threedimensional.
• When two carbon atoms are joined by a double
bond, all bonds around the carbons are in the
same plane.
– They have a flat, three-dimensional structure.
The carbon atom forms four, spatially defined hybrid sp3-orbitals instead
of the more commonly found s and p orbitals.
Tetrahedral
structure
of methane (CH4)
Rotational freedom
R1
R2
R1
C
C
R3
R2
R3
Covalent bonds
(fixed angles)
Angle = 109.5o
The carbon-carbon double bond
Ethylene
Double bond
 rigid planarity
 no free rotation possible
Chemistry based on carbon allows:
1. the creation of long carbon chains serving as the backbones of
multiple organic molecules.
2. the storage of high amounts of energy in the repetitive carbon-carbon bonds.
- for example, the C-C covalent bond contains 83.1 kcal (kilocalories) per mole,
while a C=C double covalent bond stores about 147 kcal/mole
Different carbon skeletons
Carbon & Isomers
• Isomers are compounds that have the
same molecular formula but different
structures and therefore different chemical
properties.
– For example, butane and isobutane have the
same molecular formula C4H10, but butane
has a straight skeleton and isobutane has a
branched skeleton.
• The two butanes are
structural isomers,
molecules with the
same molecular formula but differ in the
covalent arrangement of atoms.
• Enantiomers are molecules that are mirror
images of each other
– Enantiomers are possible if there are four
different atoms or groups of atoms bonded to a
central carbon.
– If this is true, it is possible to arrange the four
groups in space in two different ways that are
mirror images.
– Like left-and
right-handed
versions.
– Usually one is
biologically active,
the other inactive.
Enantiomers
 Only the L-Dopa enantiomer is effective to reduce the symptoms in
patients suffering from Parkinson Disease (PD), while the D-Dopa
isomer is biologically inactive.
The 2 stereoisomers of the amino acid alanine
Asymmetric C-atom
or
α C-atom
Only this stereoisomer of
alanine is found in biological organisms
Carbon &
Functional Groups
Carbon & Macromolecule formation
• Cells join smaller organic molecules
together to form larger molecules.
• These larger molecules, macromolecules,
may be composed of thousands of atoms
and weigh over 100,000 daltons.
• The four major classes of
macromolecules are: carbohydrates,
lipids, proteins, and nucleic acids.
Life is (vastly) polymer chemistry
• Three of the four classes of
macromolecules form chainlike molecules
called polymers.
– Polymers consist of many similar or identical
building blocks linked by covalent bonds.
• The repeated units are small molecules
called monomers.
– Some monomers have other functions of their
own.
• The chemical mechanisms that cells use to
make and break polymers are similar for all
classes of macromolecules.
• Monomers are connected by covalent bonds
via a condensation reaction or
dehydration reaction.
– One monomer provides
a hydroxyl group and
the other provides a
hydrogen and together
these form water.
– Requires energy and is
aided by enzymes.
• The covalent bonds connecting monomers
in a polymer are disassembled by
hydrolysis.
– In hydrolysis as the covalent bond is broken a
hydrogen atom and hydroxyl group from a
split water molecule attaches where the
covalent bond used to be.
– Hydrolysis reactions
dominate the
digestive process,
guided by specific
enzymes.
• Carbohydrates include both sugars and
polymers.
• The simplest carbohydrates are
monosaccharides or simple sugars.
• Monosaccharides generally have molecular
formulas that are some multiple of CH2O.
– For example, glucose has the formula C6H12O6.
• Disaccharides, double sugars, consist of
two monosaccharides joined by a
condensation reaction.
• Polysaccharides are polymers of
monosaccharides.
• Monosaccharides, particularly glucose, are
a major fuel for cellular work.
• They also function as the raw material for
the synthesis of other monomers,
including those of amino acids and fatty
acids.
1. Carbohydrates
The general sum formula for the simplest carbohydrates, or also referred to
as monosaccharides, is:
(CH2O) x n
n = 3,4,5,6 or 7
HemiacetalFormation
(in H2O)
Hexose
Haworth projections
Hexose
Anomeric forms of glucose are annotated as alpha (α) and beta (β) forms
CH2
HO
HO
O OH
1
OH
O
OH
HO
1
OH
OH
α-D-Glucose
CH2
HO
OH
β-D-Glucose
When alpha and beta anomers of glucose become involved in polymerization
reactions stereochemically different polymers, e.g. starch and cellulose,
result with very different biological functions
Chemical structures of different biologically relevant hexoses
CH2
HO
O OH
HO
CH2
OH
O
HO
HO
HO
(β-D-Mannose)
OH
OH
(β-D-Galactose)
O OH
OH
OH
HO
CH2 – OH
CH2
O
OH
O OH
HO
(β-D-Fructose)
HO
CH2
CH2
HO
OH
OH
(β-D-Glucose)
OH
O
CH3 OH
HO
OH
OH
HO
NH2
(β-D-Glucosamine)
OH
(β-L-Fucose)
= 6-Deoxy-β-L-galactose
Chemical structures of different biologically relevant mono-saccharides
Triose
Pentoses
Xylose
Arabinose
Disaccharides
 Disaccharides and polysaccharides are formed by dehydration synthesis
involving two critical hydroxyl groups of mono sugars under release of water
 The covalent bond formed between two adjacent sugar molecules in di- and
polysaccharides is also referred to as glycosidic linkage or glycosidic bond.
αlpha
α
Chemical structure of the disaccharides lactose and sucrose
Lactose
β(1  4)
β
α
α(1  2)
Sucrose
Polysaccharides & Biomass
 Polysaccharides are complex sugars made up from hundreds to millions of
mono-sugars linked together via multiple glycosidic bonds
 The polysaccharides cellulose, hemicellulose and starch are produced in huge
amounts by all green plants and algae during photosynthesis to form biomass
in a renewable fashion
“Globally green plants convert about 190 Giga tons (190 x 109 tons)
of carbon dioxide (CO2) into biomass annually.”
• Polysaccharides are polymers of hundreds
to thousands of monosaccharides joined by
glycosidic linkages.
• One function of polysaccharides is as an
energy storage macromolecule that is
hydrolyzed as needed.
• Other polysaccharides serve as building
materials for the cell or whole organism.
• Important polysaccharides are: starch
(plants), cellulose (plants), and glycogen
(animals).
Cellulose
 Cellulose is an unbranched polysaccharide build from glucose units
 8,000 – 12,000 glucose molecules are linked via β (1  4)-glycosidic bonds
“Cellulose can be broken down into smaller fragments, cellobiose and glucose
with the help of a class of enzymes called cellulases.”
Starch
 Starch is a polysaccharide composed of glucose monomers
 It consists to 20- 30% of unbranched amylose and the rest is comprised of
the branched amylopectin component
 The glucose monomers are linked via repeated 1  4-α-glycosidic linkages
“Starch can be easily broken down into smaller amylose fragments, maltose and
glucose with the help of a class of enzymes called amylases and glucoamylases.”
Starch & Human Food
 Starch is an important, high caloric component of many human
staple foods, such as French fries, tortillas, noodles and rice
 Important agricultural plants store huge amounts of starch in
different plant parts
Agricultural plant
1. sugar cane
2. sugar beet
3. corn
4. rice
5. Wheat
6. barley
7. potato
8. jam
Plant part of starch storage
stems
tuber
endosperm of kernel
endosperm of kernel
endosperm
endosperm
tuber
tuber
Hemicellulose
 Hemicellulose is a complex polymer comprised of the mono-sugars xylose,
arabinose, galactose und fucose which is found in plant cell walls
 Hemicellulose polysaccharides, are often referred to as cross-linking glycans,
since they are hydrogen bonded to the surface of the cellulose microfibrils
 It is hypothesized that hemicellulose polymers tether the cellulose microfibrils
Fats & Oils
 A fat is a polymer consisting of one glycerol backbone and three covalently
attached fatty acids; chemically fats are triacylglycerides (TAGs)
 They are high energy-containing molecules which serve as energy reserve and
play a role in thermo-insulation
 Depending on the fatty acid composition, TAGs appear as more solid fats or
more viscous oils
Two saturated fatty acids
A triacylglyceride (TAG) molecule
Fatty acid
Glycerol
Triacylglycerides & Biological functions
1. Protection from the metabolism lowering, negative effects of low temperatures
2. Avoidance of hypothermia in infants, hibernating mammals and whales.
3. High energy-donating reserve molecule, especially during periods of food
scarcity, mal-nutrition or during stress.
4. Storage and deposit layer for certain lipophilic (= fat-loving) molecules,
i.e. metabolic wastes, drugs, poisons, and pesticides
A typical phospholipid molecule
Phosphate group
Glycerol
2x Fatty acid
Space fill
structure
Chemical structure
 Phospholipids consist of two fatty acids, which are covalently linked to
a glycerol backbone (see pink-colored part).
 The third molecular component which is covalently linked with the third
hydroxyl group of the glycerol backbone can be a(n):
1. Phosphate group
2. Phosphate derivative
3. Choline
4. Ethanolamine
5. Sugar (e.g. inositol)
Polar and unpolar regions of a typical phospholipid molecule
Head
Tail
Arrangement of phospholipids in a biological (= cell) membrane
( Lipid bilayer diagram)
Schematic picture of a segment of a biological cell membrane
Steroids
 Steroids are 4-ringed, lipid-like molecules which are the starting material
for the synthesis of many important biological molecules.
 Most of the steroids, for example cholesterol, are very lipophilic molecules.
Chemical structures of different steroids
H3C
O
CH2OH
H3C C
OH
OH
O
H3C
H3C
O
H3C
H3C
CH3
CH3
H3C
HO
O
1
2
(Testosterone)
3
(Cortisone)
(Cholesterol)
Mammals & Humans
CH3
H3C
H3C
H3C
CH3
H3C
CH3
O
H3C
HO
H3C
HO
H3C
H3C
CH3
O
HO
O
4
(Ergosterol)
 Yeast steroid
Glucose
Glucose
Galactose
Galactose
Xylose
H
O
5
(Digitonin)
 Plant glycoside
 saponine
CH3
OH
HO
H
CH3
OH
H3C
OH
HO
OH
6
(Ecdysteron)
 Insect steroid
 “molting hormone”
Alcohols
 Alcohols are a class of compounds which contain the hydroxyl (-OH)
functional group and have the general formula ROH.
 An alcohol containing a –CH2OH group is known as a primary alcohol.
An alcohol which contains a =CHOH group is referred to as a secondary alcohol.
An alcohol containing a ≡COH group is a tertiary alcohol.
 Common alcohols are methanol, ethanol, propanol and butanol, which are
alcohols containing 1,2,3, and 4 carbon atoms.
 Alcohols containing two or more hydroxyl groups are called diols, triols and so on.
Properties of Some Alcohols
Name
Alcohol
Boiling Point
(oC)
Water Solubility
(g/100ml H2O);
25oC
CH3OH
Methanol
65
miscible
CH3CH2OH
Ethanol
78
miscible
CH3CH2CH2OH
1-Propanol
97
miscible
CH3CH2CH2CH2OH
1-Butanol
117
9.0
CH3CH2CH2CH2CH2OH
1-Pentanol
138
2.7
CH3CH2CH2CH2CH2CH2O
H
1-Hexanol
158
0.6
Amino acids & Proteins
Serine
Red
Blue
Cysteine
= conserved amino and carboxy group involved in peptide bond formation
= unique part or “R- group” of the amino acid
20 amino acids have been identified in all forms of life on planet Earth, which –
according to their different chemical structures - have been organized in
following groups:
 basic amino acids
=
arginine, histidine, lysiine
 acidic amino acids
=
glutamic acid, aspartic acid,
asparagine, glutamine
 aliphatic amino acids
=
glycine, alanine, leucin, isoleucine, valine
 sulfur-containing
=
cysteine and methionine
 aromatic amino acids
=
tyrosine, phenylalanine, tryptophan
 non-aromatic a. acids
=
serine, threonine
Examples of hydrophobic amino acids
Amino acids & Peptide bond formation
 Amino acids can be chemically linked together by dehydration synthesis
which results in the formation of a peptide bond.
 In living cells, this chemical reaction which leads to the formation of
polypeptides is catalyzed by a large protein/RNA complex called a ribosome.
Hierarchical organization of proteins
 The linear arrangement of amino acids in a polypeptide chain, or amino
acid sequence, is also called the primary structure of a protein.
Peptide bond
 In order for a polypeptide chain to become biologically functional it has
to be folded and coiled into a final, uniquely shaped 3-dimensional form,
called a protein.
Hierarchical organization of proteins
 Parts of the polypeptide chain of a protein are coiled or folded into two
characteristic micro-structures, referred to as secondary structures.
 Important secondary structures are:
1. Alpha-helix (plural alpha-helices)
2. Beta-sheet (or often called pleated sheets)
 Both secondary structures of are maintained/stabilized by regular spaced
hydrogen bonds between the - N – H groups and the – C = O groups at
the alpha C-atom.
α-Helix
 Hydrogen bond formation between residues of the peptide bonds
of amino acids forms a rigid, rod-like molecular cylinder.
R-Groups
Hydrogen
Bonds
β-Sheet (or pleated sheet)
 Hydrogen bonding between backbone atoms of amino acids of adjacent
-sheets form a rigid, planar, sheet-like structure in proteins.
Hydrogen
Bonds
R-Groups
Polypeptide 1
Polypeptide 2
Pleated or beta sheets
in a protein
Hierarchical organization of proteins
 The 3-dimensional structure of a protein is referred to as the tertiary structure.
 The final 3-dimensional structure of a protein is strongly dependent on:
1. The linear sequence of its amino acids and
2. The chemical properties of the side groups (R) of its amino acids
“The 3-dimensional protein structure determines the protein’s
unique biological function…”
α-Helix
β-Sheet
Loops/Turns
Computer-assisted ribbon model of the mitochondrial IDH protein depicting
the “run” of the polypeptide chain
Hierarchical organization of proteins
 When multiple polypeptide chains or protein sub-units interact to form
to form the final functional protein complex, we speak of a quaternary structure.
 Examples are: Hemoglobin, Growth factor receptors and Immunoglobulins.
Nucleotides & Nucleic acids
 Nucleic acids are made up from nitrogen-containing chemical monomers,
called nucleotides.
 The sequence of nucleotides in nucleic acids codes for the genetic information
of proteins.
 The nucleic acid DNA is the blueprint molecule of all forms of life on planet Earth.
 2 types of nucleic acids are known:
1. Dexoyribonucleic acid (DNA
- the hereditary molecule coding for the “molecular blueprint” of life
2. Ribonucleic acid (RNA)
- different types are known, e.g. rRNA, tRNA, mRNA and microRNA, each with
different biological functions
The nucleotide Cytosine
The nucleic acid DNA
Deoxyribose
HO
“Purines”
“Pyrimidines”
 Four nucleotides  A, T, C and G make up DNA
Comparison of the RNA and DNA molecules
Sugar
Nucleotides
Ribose
(A, U, G, C)
Deoxyribose
(A, T, G, C)
Biomass
 Biomass is a direct product of a biological process called
photosynthesis.
 During photosynthesis, sunlight is captured by plants and algae with
the help of chlorophyll molecules and used as energy source for
fixation of CO2 in the chemical bonds of the many carbon compounds.
“Biomass is defined as all non-fossil-based living or dead organisms and organic
materials that regrow and have an intrinsic chemical energy content.
Examples of biomass are dead or live leaves, stems, branches or trunks of trees,
shrubs, grasses, animal fat and protein and algae.”