Chemistry of Life

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Chemistry of Life
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3.1 Lifes molecular diversity is based on the
properties of carbon

• A carbon atom forms four covalent bonds
• It can join with other carbon atoms to make
  chains or rings

Structuralformula
Ball-and-stickmodel
Space-fillingmodel
Methane
The 4 single bonds of carbon point to the corners
of a tetrahedron.
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• Carbon skeletons vary in many ways

Ethane
Propane
Carbon skeletons vary in length.
Butane
Isobutane
Skeletons may be unbranched or branched.
1-Butene
2-Butene
Skeletons may have double bonds, which can vary
in location.
Cyclohexane
Benzene
Skeletons may be arranged in rings.
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3.3 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
• A huge number of different polymers can be made
  from a small number of monomers

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• Cells link monomers to form polymers by
  dehydration synthesis

1
2
3
Unlinked monomer
Short polymer
Removal ofwater molecule
1
2
3
4
Longer polymer
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• Polymers are broken down to monomers by the
  reverse process, hydrolysis

1
2
3
4
Addition ofwater molecule
1
2
3
Coating of capture strand
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Macromolecules

• Carbohydrates (simple sugar)
• Lipids (fatty acids)
• Proteins (amino acids)
• Nucleic acids (nucleotides)

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Carbohydrates

• have the general formula CH2On where n is a
  number between 3 and 6
• function in
• short-term energy storage (such as sugar)
• as intermediate-term energy storage (starch for
  plants and glycogen for animals) and
• as structural components in cells (cellulose) in
  the cell walls of plants and many protists), and
  chitin in the exoskeleton of insects and other
  arthropods.

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• The monosaccharides glucose and fructose are
  isomers

• They contain the same atoms but in different
  arrangements

Glucose
Fructose
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Carbohydrates

• Monosaccharides are single (monoone)sugars
• ribose (C5H10O5)
• glucose (C6H12O6)

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Carbohydrates

• formed when two Monosaccharides are chemically
  bonded together
• Sucrose, a common plant disaccharide is composed
  of the monosaccharides glucose and fructose.
• Lactose, milk sugar, is a disaccharide composed
  of glucose and the monosaccharide galactose.

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Dehydration reaction
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Synthesis and digestion of disaccharides
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3.6 Connection How sweet is sweet?

• Various types of molecules, including non-sugars,
  taste sweet because they bind to sweet
  receptors on the tongue

Table 3.6
http//www.cancer.gov/cancertopics/factsheet/Risk/
artificial-sweeteners
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Sweets
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Discovery

• Charles Zuker, a neuroscientist at Howard Hughes
  Medical Institute, made a startling announcement
  All the sweet things in life are perceived by two
  receptors.
• More than 30 receptors code for bitter taste but
  only a single receptor devoted to sweet.
• Bitter? there are many and many are toxic
• Sweet? all tasty and good

http//www.discover.com/issues/aug-05/departments/
chemistry-of-artificial-sweeteners/
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G-coupled Receptor Family
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G-coupled proteins

• a protein family of transmembrane receptors that
  transduce an extracellular signal (ligand
  binding) into an intracellular signal (G protein
  activation).

http//upload.wikimedia.org/wikipedia/en/3/33/G-pr
otein-coupled_receptor.png
http//en.wikipedia.org/wiki/G-protein_coupled_rec
eptor
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Receptor binding

• Sucralose, for instance, fits more snugly in the
  receptor than sucrose, partly because its
  chlorine atoms carry a stronger charge than the
  oxygen atoms they replaced.

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(Polysaccharide)

• are large molecules composed of individual
  monosaccharide units.
• The formation of the ester bond by condensation
• (the removal of water from a molecule) allows the
  linking of monosaccharides into disaccharides and
  polysaccharides.

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Carbohydrates (Polysaccharide)
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• Starch and glycogen are polysaccharides that
  store sugar for later use

• Cellulose is a polysaccharide in plant cell walls

Starch granules in potato tuber cells
Glucosemonomer
STARCH
Glycogen granules in muscle tissue
GLYCOGEN
Cellulose fibrils ina plant cell wall
CELLULOSE
Cellulosemolecules
Figure 3.7
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Starch

• starch is a combination of two polymeric
  carbohydrates (polysaccharides) called amylose
  and amylopectin. They differ in the glycosidic
  bonds they make in between glucose molecules.
• Can humans digest starch?
• What enzyme is used to digest starch?

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Glycogen

• Glycogen is a polysaccharide that is the
  principal storage form of glucose (Glc) in animal
  and human cells.
• Glycogen is found in the form of granules in the
  cytosol in many cell types.

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Glycogen

• Hepatocytes (liver cells) have the highest
  concentration of it - up to 8
• In the muscles, glycogen is found in a much
  lower concentration (1 of the muscle mass), but
  the total amount exceeds that in liver.
• Glycogen plays an important role in the glucose
  cycle.

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Glucose cycle

• When glucose enters a cell it is rapidly
  converted to glucose 6-phosphate, by hexokinase.
  The glucose cycle can occur in liver cells due to
  a liver specific enzyme glucose-6-phosphatase,
  which catalyse the dephosphorylation of glucose
  6-phosphate back to glucose.

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Insulin

• http//en.wikipedia.org/wiki/Insulin

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Glucagon

• http//en.wikipedia.org/wiki/Glucagon

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Cellulose

• Plants make it except tunicates (animals)
• Cellulose is synthesized in higher plants by
  enzyme complexes localized at the cell membrane
  called cellulose synthase

http//en.wikipedia.org/wiki/Cellulose
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Lipid

• involved mainly with long-term energy storage
• They are generally insoluble in polar substances
  such as water.
• Secondary functions of lipids are as structural
  components (as in the case of phospholipids that
  are the major building block in cell membranes)
  and as "messengers" (hormones) that play roles in
  communications within and between cells.

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Lipid

• Lipids are composed of three fatty acids
  (usually) covalently bonded to a 3-carbon
  glycerol.The fatty acids are composed of CH2
  units, and are hydrophobic/not water soluble.

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• Fats are lipids whose main function is energy
  storage

• They are also called triglycerides
• A triglyceride molecule consists of one glycerol
  molecule linked to three fatty acids

Fatty acid
Figure 3.8B
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Structure of Fatty Acids
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Saturated and unsaturated fatty acids
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• The fatty acids of unsaturated fats (plant oils)
  contain double bonds

• These prevent them from solidifying at room
  temperature
• Saturated fats (lard) lack double bonds
• They are solid at room temperature

Figure 3.8C
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Structure of Triacylglycerols (Fats)
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Synthesis of fat
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Phospholipids
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Structure of Phospholipids
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Phosphatidylcholine

• Major component of lecithin, protective sheats of
  the brain

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Phosphatidylethanolamine

• Major component of cephalin it is found
  particularly in nervous tissue such as the white
  matter of brain, nerves, neural tissue, and in
  spinal cord.
• Major phospholipid of bacteria

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Structure of Phospholipids
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Sphingomyelin

• sphingomyelin is a major component of myelin, the
  fatty insulation wrapped around nerve cells by
  Schwann cells or oligodendrocytes.
• Multiple Sclerosis is a disease characterized by
  deterioration of the myelin sheath, leading to
  impairment of nervous conduction.

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Structure of Glycolipids
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Glycolipids

• Glycolipids are carbohydrate-attached lipids.
  Their role is to provide energy and also serve as
  markers for cellular recognition.
• Ganglioside is a compound composed of a
  glycosphingolipid (ceramide and oligosaccharide)
  with one or more sialic acids (AKA
  n-acetylneuraminic acid) linked on the sugar
  chain. It is a component the cell plasma membrane
  which modulates cell signal transduction events.
  They have recently been found to be highly
  important in immunology. Natural and
  semisynthetic gangliosides are considered
  possible therapeutics for neurodegenerative
  disorders.

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3.9 Phospholipids, waxes, and steroids are
lipids with a variety of functions

• Phospholipids are a major component of cell
  membranes
• Waxes form waterproof coatings
• Steroids are often hormones

Figure 3.9
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Cholesterol in the membrane
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Cholesterol

• Cholesterol is a sterol (a combination steroid
  and alcohol) and a lipid found in the cell
  membranes of all body tissues, and transported in
  the blood plasma of all animals.

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LDL and HDL

• When doctors talk to their patients about the
  health concerns of cholesterol, they are often
  referring to "bad cholesterol", or low-density
  lipoprotein (LDL). "Good cholesterol" is
  high-density lipoprotein (HDL) this denotes the
  way cholesterol is bound in lipoproteins, the
  natural carrier molecules of the body.

http//en.wikipedia.org/wiki/Low-density_lipoprote
in
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HDL and LDL

• High-density lipoproteins (HDL) form a class of
  lipoproteins, varying somewhat in their size
  (8-11 nm in diameter) and contents, that carry
  cholesterol from the body's tissues to the liver.
• Generally, LDL transports cholesterol and
  triglycerides away from cells and tissues that
  produce more than they use, towards cells and
  tissues which are taking up cholesterol and
  triglycerides.

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Nucleic Acids

• composed of monomer units known as nucleotides.
• The main functions of nucleotides are information
  storage (DNA), protein synthesis (RNA), energy
  transfers (ATP and NAD), and signaling molecules
  (cAMP)
• Nucleotides consist of a sugar, a nitrogenous
  base, and a phosphate.

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A nucleotide
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• The monomers of nucleic acids are nucleotides

• Each nucleotide is composed of a sugar,
  phosphate, and nitrogenous base

Nitrogenousbase (A)
Phosphategroup
Sugar
Figure 3.20A
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DNA
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Polymerization of Nucleotides (Phosphodiester
bond)
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RNA
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Proteins

• They are very important in biological systems as
  control and structural elements.
• The building block of any protein is the amino
  acid, which has an amino end (NH2) and a carboxyl
  end (COOH).
• The R indicates the variable component (R-group)
  of each amino acid.

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• Each amino acid contains

• an amino group
• a carboxyl group
• an R group, which distinguishes each of the 20
  different amino acids

Aminogroup
Carboxyl (acid)group
Figure 3.12A
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• Each amino acid has specific properties

Leucine (Leu)
Serine (Ser)
Cysteine (Cys)
HYDROPHOBIC
HYDROPHILIC
Figure 3.12B
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3.13 Amino acids can be linked by peptide bonds

• Cells link amino acids together by dehydration
  synthesis
• The bonds between amino acid monomers are called
  peptide bonds

Carboxylgroup
Aminogroup
PEPTIDEBOND
Dehydrationsynthesis
Amino acid
Amino acid
Dipeptide
Figure 3.13
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Amino acids are linked together by joining the
amino end of one molecule to the carboxyl end of
another. Removal of water allows formation of a
type of covalent bond known as a peptide bond.
Formation of a peptide bond between two amino
acids by the condensation (dehydration) of the
amino end of one amino acid and the acid end of
the other amino acid.
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Protein Structure

• Primary
• Secondary
• Tertiary
• Quaternary

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Primary structure

• The primary structure of a protein is the
  sequence of amino acids, which is directly
  related to the sequence of information in the RNA
  molecule.
• The primary structure is the sequence of amino
  acids in a polypeptide.

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Secondary Structure

• It is the tendency of the polypeptide to coil or
  due to H-bonding between R-groups

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Tertiary Structure

• It occurs due to bonding (or in some cases
  repulsion) between R-groups.

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Quaternary structure

• formed from one or more polypeptides.

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3.15 A proteins primary structure is its amino
acid sequence
Primarystructure
Amino acid
Hydrogen bond
Secondarystructure
Pleated sheet
Alpha helix
Figure 3.15, 16
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3.17 Tertiary structure is the overall shape of
a polypeptide
Tertiarystructure
Polypeptide(single subunitof transthyretin)
Quaternarystructure
Transthyretin, with fouridentical polypeptide
subunits
Figure 3.17, 18