Download Hydrocarbons & Macromolecules

Hydrocarbons & Macromolecules
Mrs. Daniels
Advanced Biology
Sept. 2005
(modified Sept. 2008)
Hydrocarbons
• What are they?
• Where do we find them?
• What do we use them for?
• Old arguments of organic molecules:
vitalism vs. mechanism
Drawing Hydrocarbons
• How many bonds can carbon form?
• This enables it to form long chains
(branched or unbranched)
• Skeleton structures
• Isomers
Isomers
• Structural: same formula - different
structure or arrangement of atoms
• Ex. C2H6O
H H
H
H
|
|
H - C - C - OH
| |
H H
|
or
|
H-C-O-C-H
|
|
H
H
Isomers
• Geometric: same formula - different spatial
arrangement around double bond
• Ex. Butene C4H8
CH3
H
CH3
CH3
C = C
C = C
H
CH3
H
H
Isomers
• Optical (also called enantiomers): same
formula - mirror images of the same covalent
bonds
• Ex. Lactic acid
1
2
C
4
3
3
2
C
4
1
Naming Alkanes
• Rules to naming alkanes
• (see handout)
Saturation
• If a hydrocarbon has the greatest number
of “openings” filled with hydrogen, then it
is said to be SATURATED
• This means it is full and can hold no more
• If a hydrocarbon has a double bond, does
it have the potential to hold more
hydrogen than it has now?
• Yes…it is UNSATURATED
ATTACHMENTS TO
HYDROCARBONS
• There are many places along the
hydrocarbon chain where functional groups
can be attached
• These areas are the regions of the organic
molecule which are often chemically
reactive
• Depending on their # and arrangement,
they determine the unique chemical
properties of the molecule in which they
occur
Functional Groups
• Polar and hydrophilic:
• Hydroxyl
– An OH group
– Alcohols
• Carbonyl
– Double bonded Oxygen
– Ex. Aldehydes & ketones
Functional Groups
• Carboxyl
– An end carbon is double bonded to an O and is
single bonded to a hydroxyl group
• Amino
-weak base
-NH2
• Sulfhydryl
– SH
– Called thiols
• Phosphate
– PO4 -3
Most macromolecules are
polymers

Monomer- subunit/building block molecule of a polymer.

Polymer -poly means “many” and mer means “part”
-large molecule consisting of many identical or similar parts or subunits
connected together

Polymerization Reaction:
the process of
creating a polymer from its constituent parts
-A chemical rxn that links two or more small molecules to form
larger molecules with repeating structural units

Condensation reaction(Dehydration reaction) = most
polymerization rxns for organisms are condensation rxns.
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Monomers covalently linked, producing a net removal of
water for each covalent linkage.
One monomer loses a H+ and the other loses an OH-.
This process requires NRG and the presence of biological
enzymes and catalysts.
 Hydrolysis

= rxn that breaks the covalent bonds between
monomers by the addition of water molecules.
H bonds to one monomer and OH bonds to another
monomer thus connecting the two.
A limitless variety of polymers
can be built from a small set of
monomers

Macromolecules are: large organic polymers

4 Main Categories of Macromolecules:
Carbohydrates
Lipids
Proteins
Nucleic acids
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Unity and diversity of all life is tied to the
specific arrangement and resultant emergent
properties of these universal monomers.

There is unity in life as there are only about 40-50
common monomers used to construct all
macromolecules

There is diversity in life as new properties emerge
when these universal monomers are arranged in
different ways
Organisms use carbohydrates for fuel
and building material

Carbohydrates = organic molecules made from sugars and

their polymers.
Carbohydrates are classified according to the number of
simple sugars

Monosaccharides = simple sugars

CH2O ratio
major nutrients for cells - Glucose is most
common(produced by photosynthesis)
Chemical bond energy is harvested during cellular
respiration
carbon skeletons are the raw materials for other organic
molecules
incorporated into di and polysaccharides.
EX = triose (3 C), pentose (5 C), hexose (6 C)
Sugars end with “ose”
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Aldose- sugar with a carbonyl group at a terminal carbon
(aldehyde)
Ex. Glucose (Galactose is its enantiomer)
Ketose- sugar with carbonyl group within the carbon
skeleton (ketone)
Ex. Fructose
In aqueous solution, many form
rings

Many monosaccharides can form rings in
aqueous solns
H
O
C
H- C-OH
HO-C- H
H- C-OH
H-C-OH
H-C-OH
H
CH2OH
O
H
OH
OH
H
H
OH
H
OH

Disaccharides = two monosaccharides joined by glycosidic
linkage
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Glycosidic linkage =covalent bond formed by condensation rxn
between two sugar monomers.
Ex = maltose, lactose, sucrose
Maltose: glucose and glucose (sugar important in brewing
beer)
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Lactose: glucose and galactose (sugar present in milk)
Sucrose: glucose and fructose (table sugar; most prevalent
disaccharide)
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Polysaccharides = macromolecules made of 100s to 1000s
of monosaccharides. Enzyme mediated condensation rxns NRG storage and structural support
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Storage Polysaccharides- cells hydrolyze these into sugars as needed
 Starch- storage polysaccharide of plants- stored in
plastids(granules)
 Glycogen- glucose polymer - storage polysaccharide in animals
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Large glucose polymer - highly branched- stored in muscle & the liver
Structural Polysaccharides
 Cellulose- linear unbranched polymer- major component of
plant cell walls
 Chitin- structural polysaccharide- polymer of an amino sugar
Lipids are mostly hydrophobic
molecules with diverse functions

Lipids
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diverse group of organic compounds
insoluble in water
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1.
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hydrophobic due to many C-H bonds
variation arises from fatty acid composition, number, & arrangement
Glycerol = 3 carbon alcohol
Fatty acids (carboxylic acids)= carboxylic acid group at one end =“head”
and an attached hydrocarbon chain as a “tail”
 Saturated- no dbl bonds (solid at room temp.; animal fats)
 Unsaturated-one or more dbl bonds present (liquid; plants & fish)
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Fats, Triacylglycerol, or Triglycerides

Triacylglycerol -A fat made of 3 fatty acids bonded
to one glycerol by ester linkages (triglyceride)
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Major fxn of fat is energy storage
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Humans and other mammals stock their long-term
food reserves in adipose cells (expandable as
needed)

A gram of fat stores more than twice as much
energy as a gram of a polysaccharide such as
starch
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Phospholipids = Glycerol + 2 F.A. + phosphate

a chemical group can be attached to the phosphate
Micelle: the phospholipids will form around a nonpolar
particle with their hydrophobic (hydrocarbon) tails
towards the particle and the hydrophilic (phosphate)
head facing the water
This is how particles can be washed away
Cell Membrane: a phospholipid bilayer makes up the
majority of the cell membrane
Two layers of phospolipids arrange themselves so that
the hydrocarbon tails are facing each other and the
phosphate heads form a hydrophilic sheet on both sides
of the membrane
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Steroids =
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Lipids made of 4 fused carbon rings with various
functional groups attached
Cholesterol- (C27)
 Common component of animal cell
membranes
 Precursor to many other steroids
 Too much cholesterol can lead to
atherosclerosis (see p. 835) –
plaques build up in lining
of arteries and constrict
the blood flow
HO
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Amino acids connected= polypeptide
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Amino Acid = building block molecule of a protein
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most consisting of an asymmetric carbon
Since the AA can exist in three ionic states (weak acid, weak
base, and neutral) the pH of the solution determines the
dominant ionic state
Every AA includes the following around a central  carbon:
Hydrogen atom
Carboxyl group
Amino group
Variable R group
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There are 20 amino acids
10 are essential AA’s and must be obtained from
dietary sources because they cannot be synthesized in
the body
Amino acids exist as zwitterions - dipolar ions
Peptide bonds=covalent bond formed by a
condensation rxn that links the carboxyl group of one
amino acid to the amino group of another. N-C-CN-C-C repeating sequence
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Polypeptide chains- range in length from a few
monomers to more than a thousand with unique
linear sequences of AA
 N-terminus and C-terminus
 Polypeptide chain = polymers of AAs that are
arranged in a linear sequence and linked by
peptide bonds
Chains of 50 or less AA’s = peptide
Chains of more than 50 AA’s = protein
Proteins are molecular tools
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Proteins = macromolecule consisting of one or more
polypeptide chains folded and coiled into specific
conformations
Important functions include:
 Structural support
 storage (of amino acids)
 transport (hemoglobin)
 signaling(chemical messengers)
 cellular response to chemical stimuli(receptor proteins)
 movement(contractile proteins)
 Defense(antibodies)
 and catalysis of biochemical rxns(enzymes)
Protein’s fxn depends upon specific conformation
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Four Levels of Protein Structure
Primary- determined by genes- sequenced in lab
Secondary-regular, repeated coiling & folding of a
polypeptide backbone
 Alpha helix- helical coil stabilized by H bonding by every
4th peptide bond(found in fibrous proteins)
 Beta pleated- sheet of antiparallel chains folded into
accordion pleats- held together by intrachain or interchain
H bonds between adjacent polypeptides(some fibrous and
many globular protein cores)
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Tertiary- irregular contortions of a protein due to
bonding between side chains(R groups) superimposed
upon the primary and secondary structure- bonding is
weak interactions and covalent linkage
 Hydrophobic interaction= clustering of hydrophobic
molecules as a result of their mutual exclusion from
water
 Disulfide bridges(covalent linkage)=formed between
two cysteine monomers brought together by folding
of the protein(strong bond).
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Quaternary-protein with two or more polypeptide
chains
 Protein conformation
 **Physical and chemical conditions influence
conformation**
 -Denaturation = alteration of a protein’s native
conformation and emergent biological activity
 -Proteins can be denatured by:
 Organic solvents- turns the hydrophobic chains normally
inside the core of the protein towards the
outside- hydrophilic
chains turn away from the
solvent towards the interior of the
protein.
 Chemical agents that disrupt the H bonds, pH, ionic
bonds, and disulfide bridges.
 Excessive heat- disrupts the weak interactions with
increased thermal“agitation”.
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Protein folding- most proteins pass thru several
intermediate stages to reach their final conformation
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Chaperone proteins= newly discovered
“brace” to a folding protein- this bracing
plays an important role as a protein conforms
to its “final” 3D shape
Nucleic acids store and transmit
hereditary information

Remember that Protein conformation is
determined by primary structure.
-Primary structure, in turn is determined by
genes
-Gene = hereditary units of DNA
 Two
types of nucleic acids
1. Deoxyribonucleic acid (DNA)
 Coded information that programs all cell
activity
 Contains directions for its own replication
 Copied and passed from one generation of
cells to the next
 In Eukaryotes- found primarily in the nucleus
(but is also found in mitochondria of cells)
 Make up genes-contain instructions for
making mRNA, which in turn is responsible
for protein synthesis
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2. Ribonucleic acid (RNA)
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Functions in actual synthesis of proteins coded by
DNA
Site of protein synthesis=ribosomes in the cytoplasm
of the cell
3 main types of RNA: messenger RNA (mRNA),
ribosomal RNA (rRNA), and transfer RNA (tRNA)
mRNA carries the encoded genetic message from
nucleus to cytoplasm
Two processes : Transcription and translation (we will
examine more closely when we know more about the
cell) involve rRNA and tRNA
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A DNA strand is a polymer with an
information-rich sequence of
nucleotides
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Nucleic acid=polymer of nucleotides linked by
condensation rxns
Nucleotide=Building block molecule of a nucleic
acid
Made of :
 5 carbon sugar
 Phosphate group
 Nitrogenous base
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Pyrimidine-6 membered ring made up of
carbon and nitrogen atoms
 Cytosine(C)
 Thymine(T)-found
only in DNA
 Uracil(U)-found only in RNA
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Purine-5 membered ring fused to a 6
membered ring
 Adenine(A)
 Guanine(G)
Nucleotides have several fxns:
Many are monomers for nucleic acids
 Many transfer chemical energy from
one molecule to another (ex. ATP)
 Many are electron acceptors in enzyme
controlled redox rxns of cell
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Inheritance is based on precise
replication of DNA
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Double helix-Proposed by Watson and Crick(1953)
Rosalind Franklin
Two nucleotide chains wound in a double helix
Sugar-phosphate backbones are outside the helix
Nitrogenous bases paired in the interior of the
helix(H bonds)
Adenine to Thymine, Cytosine to Guanine pairing rule
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Two strands are complimentary thus they serve
as templates to make new strands- it is this
mechanism of precise copying that makes
inheritance possible
Most DNA molecules - 1000s to 1000000s of
base pairs long

Species that have many characteristics in
common, are found to have many of the
same DNA sequences which cause the
production of similar amino acids and
proteins
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Other structures and their functions (which
ultimately are based on the DNA code) in
many cases are very similar as well