Lect. 3 macromolecules(2)

LECT. 3
MACROMOLECULES
BIOL 144a - Cell and Molecular Biology

The Chemistry of the Cell
Can be structured around 5 principles:
1. The importance of carbon
2. The importance of water
3. The importance of selectively permeable membranes
4. The importance of synthesis by polymerization of small
molecules
5. The importance of self-assembly

Molecular Composition of Cells:
a. Water –abundant molecule (≥ 70% of total cell mass)
- it is polar and it can form H-bonds with each other or
with polar molecules
b. Inorganic ions – Na⁺, K⁺, Mg2⁺, Ca2⁺ , phosphate
(HPO42¯ , Cl¯ and bicarbonate (HCO3¯)
- 1% or less of the cell mass
- these ions are involved in number of aspects of cell
metabolism
c. Organic molecules – 80-90% of the dry weight of most
cells
- carbohydrates, lipids, proteins, and nucleic acids

The Importance of Synthesis by Polymerization
1. Macromolecules are responsible for most of
the form and function in living systems
2. Cells contain 3 different kinds of
macromolecules
• informational
• storage and
• structural
3. Macromolecules are synthesized by
stepwise polymerization of monomers

Biological Polymer
Proteins Nucleic Acids Polysaccharides
Kind of
macromolecule
Informational Informational Storage Structural
Examples Enzymes, DNA, RNA
Starch,
Glycogen
Cellulose
Hormones,
Antibodies
Repeating
monomers
Amino Acids Nucleotides
Monosacchari
des
Monosaccharid
es
Number of
kinds of
repeating units
20
4 in DNA;
4 in RNA
One or a few One or a few

Small organic molecules
Macromolecules
Supramolecular
structures
Organelles and
other structures
Hierarchical nature of cellular structures and their assembly

MACROMOLECULES
◦ Cellular structures such as ribosomes,
chromosomes, membranes, flagella, and cell walls
are made up of ordered arrays of linear polymers
or Macromolecules
◦ constructed by covalently bonding monomers by
condensation reactions where water is removed
from functional groups on the monomers.

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);
◦ intermediate-term energy storage (starch for
plants and glycogen for animals);
◦ structural components in cells (cellulose in the
cell walls of plants and many protists), and
chitin in the exoskeleton of insects and other
arthropods

CARBOHYDRATES
CLASSES OF CARBOHYDRATES
1. Monosaccharides
- simple sugars

Glucose is by far the most common carbohydrate and
classified as a monosaccharide, an aldose, a hexose, and
is a reducing sugar. It is also known as dextrose .
-also called blood sugar as it circulates in the blood at a
concentration of 65-110 mg/mL of blood.
Fructose is more commonly found together with glucose
and sucrose in honey and fruit juices. Fructose, along
with glucose are the monosaccharides found in
disaccharide, sucrose.
-the most important ketose sugar
- common name for fructose is levulose

CARBOHYDRATES
2. Disaccharides
- 2 monosaccharides/sugars
Sucrose Lactose Maltose

Disaccharide Description
Component
monosaccharides
Sucrose common table sugar glucose 1α→2 fructose
Maltose
product of starch
hydrolysis
glucose 1α→4 glucose
Lactose main sugar in milk
galactose 1β→4
glucose
Disaccharide descriptions and components
Disaccharides consist of two simple sugars

CARBOHYDRATES
3. Polysaccharides
Polysaccharides are polymers of simple
sugars
Many polysaccharides, unlike sugars, are insoluble in
water.
Dietary fiber includes polysaccharides and
oligosaccharides that are resistant to digestion and
absorption in the human small intestine but which are
completely or partially fermented by microorganisms in
the large intestine.

Oligosaccharide
- a saccharide polymer containing a small
number (typically three to ten) simple sugars
- commonly found on the plasma membrane of
animal cells where they can play a role in cell-cell
recognition.

3. Polysaccharide
3.1 Starch
Starch is the major form of stored carbohydrate in plants. Starch is
composed of a mixture of two substances:
amylose, an essentially linear polysaccharide,
and amylopectin, a highly branched polysaccharide.
Both forms of starch are polymers of α-D-Glucose.
Natural starches contain 10-20% amylose and 80-90% amylopectin.
Amylose forms a colloidal dispersion in hot water (which helps to
thicken gravies) whereas amylopectin is completely insoluble.

•Amylose molecules consist typically of 200 to 20,000 glucose
units which form a helix as a result of the bond angles between
the glucose units.

Amylopectin differs from amylose in being highly
branched. Short side chains of about 30 glucose
units are attached with 1α→6 linkages approximately
every twenty to thirty glucose units along the chain.
Amylopectin molecules may contain up to two million
glucose units.
Amylopectin The side branching chains are clustered
together within the amylopectin molecule

CARBOHYDRATES
3.2. Glycogen
- liver and skeletal muscles are major
depots of glycogen

Glycogen
Glucose is stored as glycogen in animal tissues by the
process of glycogenesis. When glucose cannot be stored as
glycogen or used immediately for energy, it is converted to fat.
Glycogen is a polymer of α-D-Glucose identical to amylopectin,
but the branches in glycogen tend to be shorter (about 13
glucose units) and more frequent. The glucose chains are
organized globularly like branches of a tree originating from a
pair of molecules of glycogenin, a protein with a molecular
weight of 38,000 that acts as a primer at the core of the
structure. Glycogen is easily converted back to glucose to provide
energy.
Glycogen

CARBOHYDRATES
(Polysaccharide)
3.3. Cellulose
- structural component

Cellulose
Cellulose is a polymer of β-D-Glucose, which in
contrast to starch, is oriented with -CH2OH groups
alternating above and below the plane of the
cellulose molecule thus producing long, unbranched
chains. The absence of side chains allows cellulose
molecules to lie close together and form rigid
structures. Cellulose is the major structural material
of plants. Wood is largely cellulose, and cotton is
almost pure cellulose. Cellulose can be hydrolyzed to
its constituent glucose units by microorganisms that
inhabit the digestive tract of termites and ruminants.
Cellulose

Chitin
Chitin is an unbranched polymer of N-Acetyl-D-
glucosamine. It is found in fungi and is the
principal component of arthropod and lower
animal exoskeletons, e.g., insect, crab, and
shrimp shells. It may be regarded as a derivative
of cellulose, in which the hydroxyl groups of the
second carbon of each glucose unit have been
replaced with acetamido (-NH(C=O)CH3) groups.
Chitin

Glycosaminoglycans
Glycosaminoglycans are found in the lubricating fluid of the joints and as
components of cartilage, synovial fluid, vitreous humor, bone, and heart
valves.
- are long unbranched polysaccharides containing repeating disaccharide
units that contain either of two amino sugar compounds -- N-
acetylgalactosamine or N-acetylglucosamine, and a uronic acid such as
glucuronate (glucose where carbon six forms a carboxyl group).
- are negatively charged, highly viscous molecules sometimes called
mucopolysaccharides.
- The physiologically most important glycosaminoglycans are hyaluronic
acid, dermatan sulfate, chondroitin sulfate, heparin, heparan sulfate,
and keratan sulfate. Chondroitin sulfate is composed of β-D-glucuronate
linked to the third carbon of N-acetylgalactosamine-4-sulfate as
illustrated here. Heparin is a complex mixture of linear polysaccharides
that have anticoagulant properties.
HeparinChondroitin Sulfate

II. Lipids
- diverse group of non-polar biomolecules
- have the ability to dissolve in organic solvents (chloroform
or benzene but not in water.
Three Major Roles in Cells
1. provide an important form of energy storage
2. as major component of cell membrane (great
importance in cell biology)
3. play important role in cell signaling as
a. steroid hormones (eg. Estrogen and testosterone)
b. messenger molecules – convey signals from cell
surface receptors to targets within the cell.

Fatty acids- consist of long hydrocarbon
chains, most frequently containing 16 or
18 carbon atoms, with a carboxyl group
(COO-) at one end
-maybe saturated or unsaturated
fatty acids

Saturated fatty Acids
- lack double bonds (eg. Stearic acid)
- common component of animal fats (solid at
room T)
Unsaturated fatty acids
- possesing double bonds
- double bonds create kinks in the molecules
- found in vegetable fats (liquid at room T)

TRIGLYCERIDES
- consist of three fatty acids linked to a
glycerol molecule
- insoluble in water and therefore accumulate
as fat droplets in the cytoplasm.
- can be broken down for use in energy-
yielding reactions (more efficient form of
energy storage than carbohydrates,
yielding more than twice as much energy
per weight of material broken down.

1. Simple lipids:
Esters of fatty acids with various alcohols.
a. Fats: Esters of fatty acids with glycerol.
Oils are fats in the liquid state.
b. Waxes: Esters of fatty acids with higher
molecular weight monohydric alcohols.

Neutral glycerides
◦ Ester of glycerol and a fatty acid.
◦ Principal function is energy storage – fat or oil.
◦ May have 1-3 fatty acids which need to be the same.
◦ 1 – monoglyceride 2 - diglyceride 3 - triglyceride

2. Complex lipids:
Esters of fatty acids containing groups in addition to
an alcohol and a fatty acid.
a. Phospholipids:
◦ Lipids containing, in addition to fatty acids and
an alcohol, a phosphoric acid residue.
◦ They frequently have nitrogen-containing bases
and other substituents
◦ in glycerophospholipids the alcohol is glycerol
◦ in sphingophospholipids the alcohol is sphingosine.

Phospholipids - principal components of cell
membrane
- are amphipathic molecules
(part water-soluble and part water-insoluble )

b. Phosphoglycerides
◦ Lipids that contain a phosphate group.
◦ Modified fat where a phosphate replaces one
of the fatty acid chain.
◦ Uses:
◦ Production of cell membranes.
◦ Emulsifying agents.

c. Nonglycerol lipids
Sphingolipids
◦ A type of phospholipid NOT derived from fat.
◦ Used primarily in nerve tissue – myelin sheath.
◦ In people, 25% of all lipids are sphingolipids.

Other complex lipids:
Lipids bound to other molecules
- Combination results in a structure.
d. Sulfolipids and aminolipids
e. Glycolipids (glycosphingolipids)
◦ Lipids containing a fatty acid, sphingosine, and carbohydrate.
f. Lipoproteins

Four major classes of plasma lipoproteins
◦ Chylomicrons
◦ Transport triglycerides from intestines to other tissue –
except kidneys.
◦ Very low-density lipoproteins (VLDL)
◦ Bind triglycerides in liver and carry them to fat tissue.
◦ Low-density lipoproteins (LDL)
◦ Carry cholesterol to peripheral tissues.
◦ High-density lipoproteins (HDL)
◦ Bound to plasma cholesterol.
◦ Transport cholesterol to liver.
Each is composed of several types of lipids.

Cholesterol:
- an important component
of cell membranes
- principal membrane lipid
for fluidity
- an amphipathic
molecule because of its
polar hydroxyl group.
- also a precursor to the
steroid hormones, such
as testosterone and
estradiol (a form of
estrogen).
g. Cholesterol

h. Steroids
◦ Broad class of compounds that all have the same
base structure.

III. Nucleic Acids
◦ informational macromolecules of the cell
◦ role in storing, transmitting, and expressing genetic
information.
◦ linear polymers of nucleotides strung
together in a genetically determined order.
◦ DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)

DNA contains instructions for:

The monomeric units of nucleic acids are
called nucleotides

The nucleoside adenosine can have one,
two, or three phosphates attached.
cv
cv
cv
Adenosine can also
form part of the
following three
nucleotides:
- AMP
- ADP
- ATP
The hydrolysis of a
phosphoanhydride
bond typically liberates
2-3x as much free
energy as does the
hydrolysis of a
phosphoester bond.

Nucleic acids consist of LINEAR CHAINS of
nucleotides
◦ Linear polymers formed
by linking each
nucleotide to the next
through a phosphate
group.
◦ Linkage: 3’, 5’
phosphodiester bridge
◦ Result: polynucleotide
DNA

◦ RNA
Ribonucleic acid
◦ single-stranded
◦ Adenine,
Guanine, and
Cytosine are also
present in RNA,
but RNA contains
Uracil in place of
thymine

Complementary pairing between
nucleic acid bases
C G T A
The carbonyl groups and nitrogen atoms of the bases are capable of
hydrogen bond formation:
C = G A = T (or U)

Polynucleotides are always synthesized in the 5′ to
3′ direction, with a free nucleotide being added to
the 3′ OH group of a growing chain.
5’ to 3’
direction
5’ to 3’
direction

Polymerization of nucleotides to
form nucleic acids
◦requires energy
◦each successive nucleotide enters as a
high-energy nucleoside triphosphate:
◦dATP, dCTP, dGTP, and dTTP (for DNA)
◦ATP, CTP, GTP, and UTP (for RNA)

Polymerization of nucleotides to
form nucleic acids
◦requires information
◦ Nucleotides must be added in a specific
sequence
◦ Template nucleotide – pre-existing DNA strand
(for both DNA and RNA synthesis).
◦ “Template-directed nucleic acid synthesis
◦Nucleic acids carry coded information
for making PROTEINS.

IV. Proteins
- Macromolecules that play important and widespread
roles in cellular structure and function.
◦ Enzymes
◦ Structural proteins
◦ Motility proteins
◦ Regulatory
proteins
◦ Transport proteins
◦ Hormonal proteins
◦ Receptor proteins
◦ Defensive proteins
◦ Storage proteins

Proteins are linear polymers of
amino acids.
◦ out of 60, only 20 amino acids are used in
protein synthesis
◦ no two different proteins have the same amino acid
sequence

Basic structure of amino
acid (AA)
All AA exist in two
stereoisomeric forms:
• D-amino acids
• L-amino acids*

Polymerization of AA
◦ The process of stringing individual amino acids together into a linear
polymer involves the stepwise addition of each new amino acid to the
growing chain by a dehydration (or condensation) reaction.
Peptide bond

◦ A protein is a polypeptide chain (or a complex
of several polypeptides) that has attained a
unique, stable, three-dimensional shape and is
biologically active as a result.
◦ “Polypeptide” – a polymer
◦ An entire polypeptide may be a monomer that is
part of a multimeric proteins
◦ Dimer – composed of 2 polypeptides
◦ Trimer - composed of 3 polypeptides
◦ Tetramer - composed of 4 polypeptides (ex. Hemoglobin)

Conformation
◦ the initial folding of a polypeptide into its
proper shape.
◦ depends on several different kinds of bonds
and interactions (important in protein folding
and stability):
◦ Disulfide bonds
◦ Hydrogen bonds
◦ Hydrophobic bonds
◦ Ionic bonds
◦ Van der Waals Interaction

Protein structure
1.primary structure
2.secondary structure
3.tertiary structure
4.quaternary structure

Primary structure
◦ the sequence of
amino acids in its
polypeptide chain
◦ Amino acid sequence of
insulin

Secondary structure- the
regular arrangement of amino acids
within localized regions of the
polypeptide.
Figure 2.19. Secondary
structure of proteins
Tertiary structure-the folding of
the polypeptide chain as a result of
interactions between the side chains
of amino acids that lie in different
regions of the primary sequence
Figure 2.20. Tertiary
structure of ribonuclease

Quaternary structure- consists of the interactions between
different polypeptide chains in proteins composed of more
than one polypeptide.
Figure 2.21. Quaternary
structure of hemoglobin

Becker’s World of the Cell – Chapter 3

Lect. 3 macromolecules(2)

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