Download Nucleic Acids

The Chemical Building Blocks of Life
Organic Chemistry
1
Comparison of Molecules
Inorganic – Chemistry of elements other than
carbon
Organic – Carbon-based chemistry
•
•
Inorganic
•Usually with
+ & - ions
•Usually
ionic bonding
•Always with
few atoms
•
Often associated with
nonliving matter
•
Organic
•Always contain
carbon and hydrogen
•Always
covalent bonding
•Often quite large, with
many atoms
•
Usually associated
living systems
•
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•
•
All living things are mostly composed of 4
elements: H, O, N, C "honk"
Compounds are broken down into 2 general
categories:
– Inorganic Compounds:
 Do not contain carbon
– Organic compounds
 Contain significant amounts of carbon.
 Often found with common "functional
groups" … more on this in a minute!
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Why Carbon?
•
Carbon is essential to
life for several reasons:
– It can form strong
stable (usually
nonpolar) covalent
bonds
– It can form up to 4
chemical bonds due to
4 valence electrons
– It can form multiple
bonds
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More on the Carbon Atom
•
Carbon atoms:
–
–
–
–
Contain a total of 6
electrons
Often bonds with
other carbon atoms to
make hydrocarbons
Can produce long
carbon chains like
octane
Can produce ring
forms like cyclohexane
5
•
Carbon skeletons vary in many ways
Ethane
Propane
Carbon skeletons vary in length.
Isobutane
Butane
Skeletons may be unbranched or branched.
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
Cyclohexane
Skeletons may be arranged in rings.
Benzene
Figure 3.1, bottom
part 6
Functional groups help determine the
properties of organic compounds
•
•
Functional groups
– specific groups of atoms attached to
carbon backbones
 retain definite chemical properties
Functional groups are the groups of atoms
that participate in chemical reactions
– Ex. Hydroxyl groups are characteristic
of alcohols
– Ex. The carboxyl group acts as an acid
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Table 3.2
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Macromolecules
•
•
•
Some molecules called macromolecules because
of their large size
Usually consist of many repeating units
– Resulting molecule is a polymer (many parts)
– Repeating units are called monomers
Some examples:
Category
•
Example
•
•
Lipids
•
Fat
•
Glycerol & fatty acids
•
Carbohydrates •Polysaccharide
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Monosaccharide
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Proteins
•
Polypeptide
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Amino acid
•
Nucleic Acids
•
DNA, RNA
•
Nucleotide
•
Subunit(s)
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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
(building blocks)
– A huge number of different polymers
can be made from a small number of
monomers
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Dehydration and Hydrolysis
•
•
•
Dehydration - Removal of water molecule
– Used to connect monomers together to make
polymers
– Polymerization of glucose monomers to make
starch
Hydrolysis - Addition of water molecule
– Used to disassemble polymers into monomer
parts
– Digestion of starch into glucose monomers
Specific enzymes required for each reaction
– Accelerate reaction
– Are not used in the reaction
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•
Cells link monomers to form polymers by
dehydration synthesis, removes OH and H
during synthesis of a new molecule.
1
2
3
Short polymer
Unlinked monomer
Removal of
water molecule
1
Figure 3.3A
2
3
4
Longer polymer
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•
Polymers are broken down to monomers
by the reverse process, hydrolysis.
(Breaks a covalent bond by adding OH and
H.)
1
2
3
4
Addition of
water molecule
1
2
3
Figure 3.3B
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The Major Organic Groups
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What you need to know:
•
•
•
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The monomer of each group…
The function of each group…
The characteristics of each group…
Unique properties of each group…
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•
Carbohydrates
Carbohydrates are loosely defined as
molecules that contain carbon, hydrogen,
and oxygen in a 1:2:1 ratio.
– monosaccharides - simple sugars
– disaccharides - two monosaccharides
joined by a covalent bond
– polysaccharides –
made of many
monosaccharide
subunits
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Function
•
Primary
Function:
Quick Energy!
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Monosaccharides are the simplest
carbohydrates
•
•
•
•
Monosaccharides are single-unit sugars
These molecules typically have a formula
that is a multiple of CH2O
Hydrogen to oxygen ratio is 2:1.
Hi Honey…
Monosaccharides
I’m home!
are the fuels for
cellular work
Figure 3.4A
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•
The monosaccharides glucose and
fructose are isomers
–
They contain the same atoms but in
different arrangements
Figure 3.4B
Glucose
Fructose
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Isomers


isomers - alternative forms of the same
substance
ex. 8 isomers of “glucose”
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Cells link single sugars to form disaccharides
•
•
Monosaccharides can join to form
disaccharides, such as sucrose
(table sugar) and maltose
(brewing sugar)
Which type of reaction
forms a disaccharide?
Glucose
Glucose
Sucrose
Figure 3.5
Maltose
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•
Polysaccharides are long chains of sugar units.
These large molecules are polymers of hundreds
or thousands of monosaccharides linked by
dehydration synthesis.
Starch granules in
potato tuber cells
Glycogen granules in
muscle tissue
Cellulose fibrils in
a plant cell wall
Glucose
monomer
STARCH
GLYCOGEN
CELLULOSE
Cellulose
molecules
Figure 3.7
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Storage polysaccharides….
•
•
Starch - plant storage
Glycogen - animal
storage
– stored in the liver
Electron micrograph of a section of a liver
cell showing glycogen deposits as
accumulations of electron dense particles
(arrows). Mitochondria are also shown.
x30,000.
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Structural Carbohydrates
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Cellulose - plants
– alpha form or beta form of ring
– animals can not digest cellulose - “fiber”
– most abundant form of living terrestrial
biomass.
Chitin - exoskeleton of
arthropods and in fungi
cell walls
– modified form of
cellulose
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Lipids: Basic Information
•
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Lipids are loosely defined
as groups of molecules
that are insoluble in water.
– Fats (triglycerides), oils,
waxes, and steroids.
Phospholipids ( a special
category) form the core
of all biological
membranes.
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Lipids
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–
–
•
Insoluble in water
Long chains of repeating CH2 units
Renders molecule nonpolar
Types of Lipids
Type
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Fats
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Oils
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Phospholipids
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Steroids
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Waxes
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Organismal Uses
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Long-term energy storage &
thermal insulation in animals
•Long-term energy storage in
plants and their seeds
•Component of plasma
membrane
•Component of plasma
membrane; hormones
•Wear resistance; retain
water
•
Human Uses
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•
Butter, lard
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Cooking oils
•
No-stick pan spray
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Medicines
•
Candles, polishes
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Lipids are hydrophobic
•
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Lipids repel water.
Ex. The cuticle of plants
is waxy. The waxy
covering makes the plant
water proof and
minimizes water loss.
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•
•
Building Blocks of Lipids
One glycerol
Three fatty acids
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Fats and Oils (triglycerides)
•
Fats and oils consist of a glycerol molecule with three
attached fatty acids (triglyceride / triglycerol).
– Saturated fats - all internal carbon atoms are
bonded to at least two hydrogen atoms
 usually a solid at room temperature
– Unsaturated fats - at least one double bond
between successive carbon atoms
 Polyunsaturated - contains more than one double
bond
 usually liquid at room
temperature
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Fats as Energy Storage Molecules
Fats, on average, yield about 9 kcal per
gram versus 4 kcal per gram for
carbohydrates.
– Animal fats are saturated while most
plant fats are unsaturated.
 Consumption of excess carbohydrates
leads to conversion into starch,
glycogen, or fats for future use.
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Triglycerides
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Saturated vs. unsaturated fatty acids
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Hydrogenated Fats
•
Hydrogenation is used to add hydrogens
to unsaturated fats and make them more
solid. If a fat is FULLY saturated, it
becomes solid, like candle wax. If it is
PARTIALLY saturated (the same as
partially hydrogenated) the result is a
semi-solid, like margarine.
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Steroids
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Steroid hormones are crucial substances for the
proper function of the body. They mediate a
wide variety of vital physiological functions
ranging from anti-inflammatory agents to
regulating events during pregnancy.
They are synthesized and secreted into the
bloodstream by endocrine glands such as the
adrenal cortex and the gonads (ovary and
testis).
Skeleton made of four fused carbon rings
Cholesterol is a steroid
as well as the foundation
for other steroids.
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Waxes

Long-chain fatty acid bonded
to a long-chain alcohol

High melting point

Waterproof

•
Resistant to
degradation
Why do you wax a car?
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Waxes
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Phospholipids
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Phospholipids
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Derived from triglycerides
– Glycerol backbone
– Two fatty acids attached instead of three
– Third fatty acid replaced by phosphate group
 The fatty acids are nonpolar and hydrophobic
 The phosphate group is polar and hydrophilic
Molecules self arrange when
placed in water
– Polar phosphate “heads”
next to water
– Nonpolar fatty acid
tails” overlap and exclude
water
– Spontaneously form double
layer & a sphere
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Phospholipid Structure
•
Phospholipid
molecules have one
end which is
attracted to water
while the other is
repelled by it. The
fatty acid end is not
attracted to water
and is called
hydrophobic. At the
other end of the
molecule the
phosphate group is
attracted to water, it
is said to be
hydrophilic.
Hydrophobic
Tail
Hydrophilic
Head
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Phospholipids Form Membranes
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Proteins
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Protein functions:
– enzyme (catalyst)
– defense
– transport
– support
– motion
– regulation
– storage
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7 Classes of Proteins
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Structural
– Spider silk
– Mammal hair
– Fibers of tendons
and lipids
Contractile
– Muscular movement
Storage
– Egg white
Defense
– Antibodies
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Transport
– Hemoglobin
Signal
– Some hormones
Chemical catalyst
– Enzymes
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Structure is related to function!
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Structurally
sophisticated.
Shape determines
function and is crucial
to the job of a protein.
Composed of amino
acids joined together
by peptide bonds.
– 20 types of amino
acids
– Made at the
ribosomes in a cell.
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•
Monomer: Amino Acids (AA)
contain an amino group (-NH2), a carboxyl
group (-COOH) and a hydrogen atom, all
bonded to a central carbon atom
– twenty common AA
grouped into five classes
based on side groups
 nonpolar AA
 polar uncharged AA
 charged AA
 aromatic AA
 special-function AA
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Structural Formulas for the 20 Amino Acids
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Amino Acids
Peptide bond links two amino acids.
– A protein is composed of one or more
long chains of amino acids linked by
peptide bonds (dipetide and
polypeptides).
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The Polypeptide Backbone
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Amino acids joined together end-to-end
–
–
–
–
COOH of one AA covalently bonds to the NH2 of the
next AA
Special name for this bond - Peptide Bond

Two AAs bonded together – Dipeptide

Three AAs bonded together – Tripeptide

Many AAs bonded together – Polypeptide
Characteristics of a protein determined by
composition and sequence of AA’s
Virtually unlimited number of proteins
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Protein Structure
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Protein function is determined
by its shape.
The shape is driven by a number
of noncovalent interactions
such as hydrogen bonding.
Protein structure
 primary - specific amino
acid sequence
 secondary - folding of
amino acid chains
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Protein Structure


tertiary - final
folded shape of
globular protein
quaternary - forms
when two or more
polypeptide chains
associate to form a
functional protein
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Summary: Levels of Structure
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Primary:
– Literally, the sequence of amino acids
– A string of beads (up to 20 different colors)
Secondary:
– The way the amino acid chain coils or folds
– Describing the way a knot is tied
Tertiary:
– Overall three-dimensional shape of a polypeptide
– Describing what a knot looks like from the outside
Quaternary:
–
–
Consists of more than one polypeptide
Like several completed knots glued together
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Levels of Protein Organization
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Examples of Fibrous Proteins
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How enzymes work…Induced Fit Model
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The substrate (what the enzyme is going to
work upon) comes into contact with the active
site of the enzyme.
The enzyme “wraps” around the substrate
breaking or forming bonds.
The product is released.
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Enzyme at work
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Unfolding Proteins
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Denaturation refers to
the process of changing
a protein’s shape.
– usually rendered
biologically inactive
 salt-curing and pickling used to
preserve food
 temperature - high temperatures break
bonds.
 pH - designed to work at a specific pH!
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Examples
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You can not use fresh pineapple in jello but you
can used canned! Why?
Pepsin is an enzyme that helps break down
proteins in the stomach during digestion. It
works at a pH of 2!
Trypsin is an enzyme that helps break down
proteins as well. It works in the intestines with
a pH of 8.
Many snake venoms are enzymes that work when
directly injected into blood or tissue (pH = 7.4).
If swallowed, they are denatured by the acidity
of the stomach! (Don’t try it, just take my word
for it!)
Why do people without refrigeration salt their
food for long term storage?
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Nucleic Acids
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Nucleic Acids
•
•
Deoxyribonucleic Acid (DNA)
– Encodes information used to assemble
proteins.
Ribonucleic Acid (RNA)
– Reads DNA-encoded information to
direct protein synthesis.
Adenosine triphosphate
(ATP)
–
Provides energy
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•
Nucleic Acid Structure
Nucleic acids are composed of long
polymers of repeating subunits,
nucleotides - the monomer.
– five-carbon sugar
– phosphate
– nitrogenous base
 purines
 adenine and guanine
 pyrimidines
 cytosine, thymine, and uracil
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Nucleic Acid Structure
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•
DNA exists as double-stranded molecules.
– Genetic info. - coded for by the order of the
nucleotides.
– double helix
– complementary base pairing
 hydrogen bonding
 base pairing: A-T, C-G
RNA exists as a single stand.
– contains ribose instead of deoxyribose
– contains uracil in place of thymine
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Nucleotides
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Comparison of DNA & RNA
Feature
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Sugar
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Bases
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Strands
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Helix
•
DNA
Deoxyribose
RNA
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Ribose
Cytosine, guanine;
•Cytosine, guanine;
adenine, thymine
•adenine, uracil
•Double-stranded;
Pairing across strands •Mostly single stranded
•
•
Yes
Heredity; cellular
•Function control center
•Chromosomes of cell
•Where
nucleus
•
•
No
Interprets genetic info;
protein synthesis
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Cell nucleus and cytoplasm
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Structure of DNA
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RNA Structure
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DNA 
RNA
Protein
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Other Nucleic Acids
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•
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ATP (adenosine triphosphate) is composed of
adenine, ribose, and three phosphates
In cells, one phosphate bond is hydrolyzed –
Yields:
–
The molecule ADP (adenosine diphosphate)
–
An inorganic phosphate molecule pi
–
Energy
Other energy sources used to put ADP and pi
back together again
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ATP
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Summary
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Biological Molecules (contain Carbon)
– Macromolecules (polymers made of *monomers)
 Proteins (*amino acids)
 Polypeptides
 Enzymes
 Nucleic Acids (*nucleotides)
 DNA and RNA
 Lipids (*glycerol + 3 fatty acids)
 Fats, Oils, Waxes, Steroids, and
Phospholipids
 Carbohydrates (*monosaccharides)
 Monosaccharides, Disaccharides, and
Polysaccharides (Starch, Glycogen,
Cellulose, and Chitin)
70
Summary
and
Enzymes
Phosphate
group
Not all inclusive!
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