This document provides an overview of macromolecules and their importance in cellular structure and function. It discusses the five key principles of cellular chemistry: the importance of carbon, water, selectively permeable membranes, synthesis by polymerization, and self-assembly. The main macromolecules found in cells are then summarized: carbohydrates, lipids, nucleic acids, and proteins. Carbohydrates include monosaccharides, disaccharides, and polysaccharides like starch, glycogen, cellulose, and chitin. Lipids are categorized based on their structure and function. Nucleic acids DNA and RNA are composed of nucleotides and carry genetic information. Proteins are linear polymers of amino acids that serve important roles in cells
2. 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
3. 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
4. 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
5. 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
7. 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.
8. 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
10. 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
12. 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
13. 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.
14. 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.
15. 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.
16. •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.
17. 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
19. 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
21. 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
22. 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
23. 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
24. 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.
25. 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
26. 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)
28. 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.
29. 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.
30. 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
31. 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.
32. Phospholipids - principal components of cell
membrane
- are amphipathic molecules
(part water-soluble and part water-insoluble )
33. 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.
34. 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.
35. 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
36. 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.
37. 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
38. h. Steroids
◦ Broad class of compounds that all have the same
base structure.
39. 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)
43. 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.
44. 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
45. ◦ RNA
Ribonucleic acid
◦ single-stranded
◦ Adenine,
Guanine, and
Cytosine are also
present in RNA,
but RNA contains
Uracil in place of
thymine
46. 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)
47. 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
48. 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)
49. 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.
50. 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
51. 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
52. Basic structure of amino
acid (AA)
All AA exist in two
stereoisomeric forms:
• D-amino acids
• L-amino acids*
53.
54. 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
55.
56. ◦ 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)
57. 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
59. Primary structure
◦ the sequence of
amino acids in its
polypeptide chain
◦ Amino acid sequence of
insulin
60. 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
61. 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
carbon atom -the backbone of biologically important molecules.
water molecule -the universal solvent of living systems.
Membranes are differentially permeable to specific solutes, they also control the movements of molecules and ions into and out of cells and cellular compartments.
4. Synthesis of biological macromolecules by polymerization of monomers (linking together of many similar or identical small molecules).
5. Self-assembly of proteins and other biological macromolecules into higher levels of structural organization.
Fats and oil
Both are triglycerides.
Fats – Typically obtained from animals, solids at room temp, made from saturated fatty acids.
Oils – typically obtained from plants; Liquids at room temp; made from unsaturated fatty acids.
Waxes – water insoluble and hard to hydrolyze
Often used to provide a protective coating (leabes, skin, fur, hair…)
Bees wax and sebum are examples.
Ester of fatty acid and a long chain alcohol.
Figure 2.7. Structure of phospholipids Glycerol phospholipids contain two fatty acids joined to glycerol. The fatty acids may be different from each other and are designated R1 and R2.
The third carbon of glycerol is joined to a phosphate group (forming phosphatidic acid), which in turn is frequently joined to another small polar molecule (forming phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, or phosphatidylinositol). In sphingomyelin, two hydrocarbon chains are bound to a polar head group formed from serine instead of glycerol.
Cholesterol
Associated with hardening of the arteries.
Appears to coat arteries – plaque formation.
Results in creased blood pressure from:
Narrowing of arteries
Reduced ability to stretch
Clot formation leading to myocardial infarction
Sroke
Nucleic Acids - macromolecules of paramount importance to the cell because of their role in storing, transmitting, and expressing genetic information.
Transcription: A specific segment of a DNA molecule known as a gene directs the synthesis of a complementary molecule of messenger RNA (mRNA).Each gene contains the information to produce a specific polypeptide using this mRNA.
mRNA export: Following processing to remove introns (and in some cases RNA editing to alter specific bases), the mRNA leaves the nucleus through nuclear pores—tiny channels in the nuclear membrane—and enters the cytoplasm.
Translation (polypeptide synthesis): A ribosome attaches to the mRNA to read the coded information. As the ribosome moves down the mRNA, transfer RNA (tRNA) molecules bring the correct amino acids to be added to the growing polypeptide chain in the order specified by the information in the mRNA.
DNA strands are composed of monomers called nucleotides; these often are referred to as bases because their structures contain cyclic organic bases
Each nucleotide consists of a five-carbon sugar to which is attached a phosphate group and a nitrogen-containing aromatic base.
The phosphate is joined by a phosphoester bond to the 5’ carbon of the sugar
and the base is attached to the 1’ carbon.
Phosphate
The sugar is either D-ribose (in RNA) or D-deoxyribose (in DNA).
Cyclic organic base: The base may be either a purine or a pyrimidine.
DNA contains the purines adenine (A) and guanine (G) and the pyrimidines cytosine (C) and thymine (T).
RNA also has adenine, guanine, and cytosine, but it contains the pyrimidine uracil (U) in place of thymine.
Without the phosphate, the remaining base-sugar unit is called a nucleoside.
Each pyrimidine and purine may therefore occur as the free base, the nucleoside, or the nucleotide.
Adenosine occurs as the free nucleoside.
Adenosine can also form part of the following three nucleotides:
AMP
ADP
ATP
“Energy-rich compounds” - ATP
The hydrolysis of a phosphoanhydride bond typically liberates two to three times as much free energy as does the hydrolysis of a phosphoester bond.
The polynucleotide formed by this process has an intrinsic directionality, with a 5’ phosphate group at one end and a 3’ hydroxyl group at the other end.
By convention, nucleotide sequences are always written from the 5’ end to the 3’ end of the polynucleotide because this is the direction of nucleic acid synthesis in cells.
serve as enzymes - catalysts that greatly increase the rates of the thousands of chemical reactions on which life depends.
Enzymes that facilitate the many covalent bond-making and bond-breaking reactions.
Enzymes that catalyze all of the reactions whereby cells extract energy from food molecules,
Structural proteins - used to build structural components
provide physical support and shape to cells and organelles, giving them their characteristic appearances
tubulin, a protein that self-assembles to make the cell’s long microtubules
histones, proteins that compact the DNA in chromosomes.
Motility proteins - play key roles in the contraction and movement of cells and intracellular structures, act as molecular motors to produce force and movement,
as for actin and myosin in muscle
Regulatory proteins - responsible for control and coordination of cellular functions, ensuring that cellular activities are regulated to meet cellular needs.
Transport proteins are involved in the movement of other substances into, out of, and within the cell.
Hormonal proteins mediate communication between cells in distant parts of an organism
receptor proteins enable cells to respond to chemical stimuli from their environment
Defensive proteins provide protection against disease (antibodies)
Storage proteins serve as reservoirs of amino acids.
Unique - although most proteins contain all or most of the 20 amino acids at varying proportions
Every amino acid has the basic structure, with a carboxyl group, an amino group, a hydrogen atom, and a side chain known as an R group.
All are attached to a central carbon atom known as the a carbon.
Both D- and L-amino acids exist in nature, but only L-amino acids occur in proteins.
Hydrophobic amino acids are usually found in the interior of the molecule as a polypeptide folds into its three-dimensional shape.
the whole protein (or the hydrophobic portion of the molecule) is excluded from aqueous environments and instead found in hydrophobic locations, such as the interior of a membrane.
The remaining 11 amino acids have hydrophilic R groups that are either distinctly polar or actually charged at the pH values characteristic of cells.
the three atoms comprising H2O are removed
the carboxyl carbon of one amino acid and the amino nitrogen of a second are linked directly
This covalent C—N bond linking two amino acids is known as a peptide bond
Notice that the chain of amino acids formed in this way has an intrinsic directionalitybecause it always has an amino group at one end and a carboxyl group at the other end.
The end with the amino group is called the N- (or amino) terminus, and the end with the carboxyl group is called the C- (or carboxyl) terminus.
Although the process of elongating a chain of amino acids is often called protein synthesis.
the term is not entirely accurate because the immediate product of amino acid polymerization is not a protein but a polypeptide.