Download Macromolecules

Macromolecules
Molecules in the Cell
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What’s in a cell?
• Water
• Ions like Na+, Cl-,
Ca2+, PO43-, etc.
• Macromolecule
subunits and
precursors
• Macromolecules
themselves
• Other small
organic molecules:
enzyme co-factors,
secondary
metabolites.
Four Types of Macromolecule
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“Macromolecule” means “large molecule”
Macromolecules are formed from subunits. The subunits are monomers that
are joined into a polymer.
All cells use the same 4 types of macromolecules, with the same subunits.
Macromolecules have a specific sequence of different type of monomers
(especially proteins and nucleic acids).
Macromolecules also have a specific polarity: a beginning and an end.
Synthesis and Breakdown
• All of the major types of
macromolecule are
synthesized through
dehydration reactions:
removal of H2O from the two
molecules being joined
together.
– Synthesis requires energy input:
going from monomers to a
polymer is a large reversal of
entropy
• Breakdown of the
macromolecules into their
subunits occurs by the
reverse reaction: hydrolysis.
In hydrolysis, H2O is added to
the bond to break it.
Carbohydrates
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Carbohydrates are macromolecules
composed of simple sugars
(monosaccharides).
A monosaccharide’s composition has a
ratio of 1 carbon to 2 hydrogens to 1
oxygen: (CH2O)n. The simple sugars in
living cells have between 3 and 7
carbons, most commonly 5 or 6.
– Sugars are often described by the number of
carbons: pentose = 5 carbons, hexose = 6
carbons, etc.
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Monosaccharides contain several –OH
groups and either an aldehyde or a
ketone group.
– Aldoses have an aldehyde group; ketoses
have a ketone group.
– Sometimes other functional groups are also
attached: amino, carboxylic acid, etc. For
example, glucosamine and glucuronic acid,
both derived from glucose.
Sugar Rings
• In aqueous solutions, the C=O group
(aldehyde or ketone) reacts with the
second-to-last C-OH to form a ring. Sugars
can be drawn as linear structures or as
rings, but in the cell, they are mostly rings.
– Note that the 6 member hexose ring
contains 5 carbons and one oxygen, with
the sixth carbon outside the ring.
– The rings are not planar (as in benzene),
but rather they are usually found in a bent
configuration (“chair” configuration).
Sugar Stereoisomers
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Many simple sugars differ from each other in the configuration of their –OH groups.
Otherwise, these compounds are identical.
Hexoses contain 4 asymmetric carbons (carbons with 4 different groups attached). Each
asymmetric carbon generates a lefthanded and a righthanded stereoisomer.
These stereoisomers are all recognizably different: enzymes in the cell treat them
differently.
– Note that these are all diastereomers: not mirror images
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Below is the set of all D-aldose hexoses. This group includes glucose, galactose, and
mannose, which are used in the cell.
– There also exist mirror images of each: the enantiomers, with names like L-allose, L-glucose,
etc.
Sugars Forming Bonds
• Sugars bond with other sugars through a
dehydration reaction. The sugars are separated
by hydrolysis, the reverse of dehydration.
• Most sugar-sugar bonds are between the 1carbon (at the right end of the ring) and the 4carbon (at the left end).
• The –OH on the 1-carbon can be in the alpha
configuration (pointing down) or the beta
configuration (pointing up). This leads to alpha
1,4 linkages and beta 1,4 linkages. The
difference is very important: the only difference
between starch (readily digestible) and cellulose
(indigestible) is that the glucoses in starch are
linked alpha 1,4 and the glucoses in cellulose are
linked beta 1,4.
• Some also bond between the 1-carbon and
the 6-carbon (outside the ring).
Sugar Compounds
• Disaccharides: 2 sugars
– Maltose (glucose + glucose)
– Lactose (galactose + glucose)
– Sucrose (glucose + fructose)
• Oligosaccharides and
polysaccharides: chains linked mostly
1,4, but with branches using 1,6
linkages. Oligosaccharides are shorter
than polysaccharides, but the
distinction is minor.
• Complex oligosaccharides are often
attached to proteins or lipids on the
cell surface: glycoproteins and
glycolipids. Often involve many
different simple sugars.
Function of Carbohydrates
• Two main functions: food storage and structure.
• Most organisms use glucose as the primary food molecule, converting many
other compounds into glucose, then burning it in the processes of glycolysis
and respiration.
– Glucose can easily be stored as a polymer. In plants this is starch, which is
mostly linear chains of glucose. In animals, glycogen is more highly
branched chains of glucose.
• Cellulose is the main component of plant cell walls.
• Chitin forms the exoskeleton of insects and also the cell walls of fungi.
• Peptidoglycan forms the cell walls of bacteria. Peptidoglycan ties linear
chains of sugars together with short peptides.
Lipids
• Lipids are the main
hydrophobic
molecules in the cell.
• Most lipids are
composed of fatty
acids attached to
glycerol, but other
types include
steroids, waxes, and
isoprene compounds.
Lipids: Glycerol + Fatty Acids
• Fatty acids are long linear hydrocarbon
chains with a carboxylic acid group (COOH)
attached to one end. Hydrocarbons are
carbon atoms linked together, with
hydrogens attached to all the unused
bonds.
– The hydrocarbon chains are usually
between 12 and 20 carbons long
• Glycerol is a 3 carbon sugar.
– If each of the –OH groups is attached to a
fatty acid, it is a triacylglyceride
(triglyceride), used for long term food
storage.
– If 2 of the glycerol –OH’s are attached to
fatty acids, and the third is attached to a
phosphate group, it is a phosopholipid, the
main component of cell membranes.
Fatty Acid Saturation
• Fatty acids are saturated if all the carboncarbon bonds are single bonds, which
implies that maximum number of
hydrogens are attached.
• Unsaturated fatty acids contain one or
more carbon-carbon double bonds, which
means fewer hydrogens can be attached.
• C=C bonds are rigid and planar. This
means that the next carbons in the chain
can come in from the same side (cis) or
opposite sides (trans).
– In the cell, most are cis. Trans fatty acids are
made by artificially adding H’s to some (but not
all) double bonds in unsaturated fats, to make
them solid (like margarine).
Consequences of Saturation
• Saturated fatty acids are very
linear. In contrast, a cis bond in an
unsaturated fatty acid puts a kink
in the chain.
• Saturated fatty acids can pack very
tightly together. This makes them
solid at room temperature: butter
and lard, for example.
• Cis-unsaturated fatty acids don’t
pack together well, so they are
liquid at room temperature: things
like vegetable oils.
Phospholipids and Cell Membranes
• Phospholipids are composed of 2 fatty
acids attached to glycerol, with the third
position on the glycerol having a
phosphate group that has a small polar
molecule such as choline attached to it.
• This structure makes the molecule
amphipathic: one end is hydrophilic and
the other end is hydrophobic.
• When put in water, the hydrophilic ends
sit facing the water, and the hydrophobic
ends cluster together to avoid the water
molecules. This produces the bilayer
structure of the cell membrane.
– The center of the membrane is
hydrophobic, which makes it very hard for
most molecules dissolved in water to get
through.
Other Lipids
• Steroid compounds consist of 4 carbon
rings attached in a specific way, with
various side groups attached.
– The most important steroid is cholesterol, a
component of cell membranes
– Many hormones are steroids.
• Isoprene is a 5 carbon compound that
can be polymerized in many ways to
form things like rubber, scents, waxes.
Proteins
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The most important type of
macromolecule.
Roles:
Structure: collagen in skin, keratin in
hair, crystallin in eye.
Enzymes: all metabolic
transformations, building up,
rearranging, and breaking down of
organic compounds, are done by
enzymes, which are proteins.
Transport: oxygen in the blood is
carried by hemoglobin, everything
that goes in or out of a cell (except
water and a few gasses) is carried by
proteins.
Also: nutrition (egg yolk), hormones,
defense, movement
Amino Acids
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Amino Acids are the subunits of proteins.
Each amino acid contains an amino group (NH2) and an acid group (-COOH). These
groups are attached to a central carbon, called
the alpha carbon.
Each amino acid also has an R-group, which is
different for each of the 20 amino acids used
in cells.
Amino acids are joined by a dehydration
reaction. The bond between them is called a
peptide bond, and a chain of amino acids is
called a polypeptide.
Proteins consist of one or more polypeptides,
sometimes with additional small molecules
attached.
The polypeptide subunits of a protein are
attached by non-covalent bonds, including
hydrogen bonds, electrostatic interactions,
and Van der Waals forces.
R-Groups
• There are 20 different kinds of
amino acids in proteins. Each
one has a functional group (the
“R group”) attached to it.
• Different R groups give the 20
amino acids different
properties. They can be
classified in many ways, but we
will stick to: acidic, basic, polar
(hydrophilic) and non-polar
(hydrophobic).
– Some amino acids don’t fit neatly
into these categories.
• The different properties of a
protein come from the
arrangement of the amino
acids.
Charged Amino Acids
• Amino acids whose R group
carries a + or – charge at neutral
pH.
• Basic amino acids all have some
version of an amino group (-NH2),
which picks up an H to become –
NH3+.
– Lysine, arginine, and histidine.
• Acidic amino acids (aspartic acid
and glutamic acid) have a
carboxylic acid (-COOH) group,
which loses an H to become –COOat physiological pHs.
Hydrophobic
• Hydrophobic amino acids
are non-polar, and are
mainly found in the interior
of proteins, or the
hydrophobic region inside
membranes.
• Some of them are aromatic
(with benzene rings), while
others just have
hydrocarbon (aliphatic) R
groups.
Uncharged Hydrophilic R groups
• Uncharged hydrophilic amino acids are polar, due to C-N, or C-O bonds.
They are mainly found on the surface of proteins, facing the aqueous
medium.
• The acidic and basic amino acids are also polar and usually found on the
protein surface.
Protein Structure
• After the polypeptides are
synthesized by the cell, they
spontaneously fold up into a
characteristic conformation which
allows them to be active. The proper
shape is essential for active proteins.
– For most proteins, the amino acids
sequence itself is all that is needed to
get proper folding, but some need
help from chaperone proteins.
• Proteins fold up because they form
hydrogen bonds between amino
acids. The need for hydrophobic
amino acids to be away from water
also plays a big role. Similarly, the
polar amino acids need to be
exposed to water. Also, the charged
amino acids often bond by
electrostatic interactions.
Proteins
• The joining of polypeptide subunits
into a single protein also happens
spontaneously, for the same
reasons.
• Enzymes are usually roughly
globular, while structural proteins
are usually fiber-shaped. Proteins
that transport materials across
membranes have a long segment of
hydrophobic amino acids that sits in
the hydrophobic interior of the
membrane.
• Denaturation is the destruction of
the 3-dimensional shape of the
protein. Denaturation inactivates
the protein, and makes it easier to
destroy. This is the effect of
cooking foods.
Various Proteins
Collagen
Enolase
Myosin
ATP Synthase
Transmembrane peptide
transporter
Nucleic Acids
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Nucleotides are the subunits of nucleic acids
Nucleic acids store genetic information in the
cell. They are also involved in energy and
electron movements.
The two types of nucleic acid are RNA
(ribonucleic acid) and DNA (deoxyribonucleic
acid).
Each nucleotide has 3 parts: a sugar, a
phosphate, and a base.
The sugar, ribose in RNA and deoxyribose in
DNA, contain 5 carbons (pentoses). They differ
only in that an –OH group in ribose is replaced
by a –H in DNA.
– The –OH group is much more reactive than just
an –H, which is one reason DNA is more stable
than RNA.
• The carbons in the sugar are numbered
from 1’ to 5’ (1-prime to 5-prime).
– The base attaches to the 1’ carbon
– The phosphate is attached to the 5’ carbon
– New nucleotides are added to the 3’ carbon
Bases
• The bases are rings that contain both carbon
and nitrogen. The purines have 2 joined
rings and the pyrimidines are a single ring.
• The purines in DNA and RNA are adenine (A)
and guanine (G).
• The pyrimidines in DNA are cytosine (C) and
thymine (T); in RNA they are cytosine (C) and
uracil (U).
– Thymine and uracil are almost identical,
except that thymine has an extra methyl
(-CH3) group attached.
• The base is attached to the 1’ carbon of
ribose or deoxyribose, using the nitrogen at
the bottom of the pyrimidine ring, or the
nitrogen at the bottom of the 5 member
purine ring.
Pyrimidines
Phosphates
• Nucleotides can have 1, 2, or 3 phosphates attached in a
chain to the 5’ carbon of the sugar. These are
monophosphate (MP), diphosphate (DP), and triphosphate
(TP).
• After being polymerized into DNA or RNA, only 1 phosphate
remains. Removal of the other two phosphates generates
the energy needed for polymerization.
Nomenclature
• When a base is joined to a sugar, with no
phosphates, the molecule is called a
nucleoside. The nucleosides are named
adenosine, guanosine, cytidine, uridine and
thymidine.
• When one or more phosphates is added, you
have a nucleotide.
– The number of phosphates is indicated in the
nucleotide’s symbol; for example, ATP is adenosine
triphosphate, and CMP is cytidine monophosphate.
• Nucleotides can be deoxyribonucleotides,
symbolized by a small d: dATP is deoxy
adenosine triphosphate.
• If the nucleotides have ribose, they are
ribonucleotides, which are symbolized
without any addition: ATP is a
ribonucleotide.
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Adenine = base only
Adenosine = base + sugar
(nucleoside)
Adenosine monophosphate
(AMP) = base + sugar + phosphate
(nucleotide)
Nucleic Acid Synthesis
• Nucleotides are joined by a
phosphodiester linkage, between the
3’ carbon of one sugar and the 5’
carbon of the next sugar in the chain.
• The synthesis reaction is a dehydration
reaction.
• Individual nucleotides are added to a
growing chain or DNA or RNA. The raw
materials are nucleoside
triphosphates. Two of the phosphates
are removed and the innermost
phosphate is attached to the free 3’ –
OH group at the end of the growing
chain.
– The chain is said to grow from 5’ to 3’. The
5’ end is the beginning and the 3’ end is the
end of a DNA or RNA molecule.
DNA and RNA
• DNA uses 4 different bases: adenine,
guanine, thymine, and cytosine.
• The backbone of a DNA strand is a chain of
alternating sugars and phosphates. Two
antiparallel DNA strands are twisted into a
double helix It is held together by hydrogen
bonds that connect the complementary
bases in the center of the molecule.
– A pairs with T, and G pairs with C.
– DNA is a stable molecule which can survive
thousands of years under proper conditions
• RNA consists of a single chain that also uses 4
bases: however, the thymine in DNA is
replaced by uracil in RNA. RNA is much less
stable than DNA, but it can act as an enzyme
to promote chemical reactions in some
situations.
– Some of the bases in RNA pair with each
other, giving each RNA molecule a
characteristic shape.
Other Nucleic Acids
• The main energy-carrying molecule in
the cell is ATP. ATP is an RNA
nucleotide with 3 phosphate groups
attached to it in a chain. The energy is
stored in the phosphoanhydride bonds
between the phosphates.
• Several coenzymes (small molecules
that are used by enzymes) are built
from nucleotides. For example,
coenzyme A, which is used in
generating energy from glucose. It is a
modified ADP molecule.
• Some nucleotides are used in signalling
pathways. For example, cyclic AMP.
Extra
Two Special Amino Acids
• Cysteine has an –SH group at the
end of its R group. Two cysteines
can be covalently bonded by
oxidizing their –SH groups to a
single –S-S- , which is called a
disulfide bond.
– Disulfide bonds help give a protein
its three dimensional structure
• Proline has an R group that is
attached to the amino acid’s amino
group. This structure introduces a
kink in the polypeptide chain.