The document discusses the chemical composition of the human body. It describes atoms and their components, including protons, neutrons, and electrons. It explains how elements are formed from combinations of atoms, and the four most important elements for living organisms: carbon, nitrogen, oxygen, and hydrogen. It also discusses chemical bonds, including covalent and ionic bonds, and how molecules and compounds are formed through these bonds. Finally, it provides an overview of the main classes of organic molecules that make up the human body: lipids, carbohydrates, proteins, and nucleic acids.

1. Chapter 2
Chemical Composition of the
Body

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Atoms
 Smallest units of matter that can
undergo chemical change.
 Nucleus (center) contains:
 Protons (+ charge)
 Neutrons (no charge)
 Atomic mass:
 Sum of protons and neutrons.

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Atoms
 Atomic Number
 Number of protons in an atom
 Neutral atom
 Number of protons = number of electrons
 Isotopes
 Vary in number of neutrons
 Same in atomic number
 Vary in atomic mass

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Atoms
 Chemical element
 Includes all of the isotopic forms of a given
atom
 Eg: Element Hydrogen: 3 isotopes

Most common: one proton

Deuterium: one proton, one neutron

Tritium: one proton, two neutrons
 Commonly used in research
 106 chemical elements

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Elements
 Four elements important to living
organisms
 Carbon (C)
 Nitrogen (N)
 Oxygen (O)
 Hydrogen (H)

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Atoms
 Electrons (outside the nucleus):
 - charged
 Occupy orbitals surrounding nucleus.
 Valence electrons:
 Electrons in the outer most orbital that
participate in chemical reactions (if orbit
incomplete).
 Form chemical bonds.

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Orbitals
 Also called shells or energy levels
 Electrons usually found within a given
orbital
 Levels (and max number of electrons)
 First shell: 2 electrons
 Second shell: 8 electrons
 Third shell: usually 8 electrons

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Molecules, and Ionic
Compounds
 Chemical bonds:
 Interaction of valence electrons
between 2 or more atoms.
 # bonds determined by # electrons
needed to complete outer orbital.

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Covalent Bonds
 Atoms share their valence
electrons.
 Nonpolar bonds:
 Electrons are equally distributed
between the two identical atoms.
 Strongest bond.
 H2

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Covalent Bonds
 Polar bonds:
 Electrons are shared between two
different atoms.
 Electrons may be pulled more toward
more atom.
 Oxygen, nitrogen, phosphate pull
electrons towards themselves.

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Ionic Bonds
 One or more valence electrons
from an atom are completely
transferred to a second atom.
 First atom loses electrons, +
charged (cation).
 Second atom has more electrons,
- charged (anion).

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Ionic Bonds
 Cation and anion attract, form ionic
compound.
 Weaker than polar bonds.
 Dissociate easily when dissolved in
H20.
 NaCl Na+
and Cl-

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Table Salt, an Ionically Bonded Molecule
Slide number: 1
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17p
18n
11p
12n
11p
12n
17p
18n+
(+)
(–)
Na Cl+ NaCl

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Table Salt, an Ionically Bonded Molecule
Slide number: 2
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17p
18n
11p
12n
Na Cl+

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Table Salt, an Ionically Bonded Molecule
Slide number: 3
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17p
18n
11p
12n
Na Cl+

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Table Salt, an Ionically Bonded Molecule
Slide number: 4
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17p
18n
11p
12n
Na Cl+

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Table Salt, an Ionically Bonded Molecule
Slide number: 5
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17p
18n
11p
12n
Na Cl+

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Table Salt, an Ionically Bonded Molecule
Slide number: 6
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17p
18n
11p
12n
Na Cl+
(+) (–)

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Table Salt, an Ionically Bonded Molecule
Slide number: 7
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NaCl
11p
12n
(+)
17p
18n
(–)

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Interaction with water
 Hydrophilic:
 Formation of hydration spheres.
 Polar covalent bonds.
 Hydrophobic:
 Cannot form hydration spheres.
 Nonpolar covalent bonds.

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Hydrogen Bond
 Hydrogen forms a
polar bond with
another atom,
hydrogen has a
slight + charge.
 Weak attraction
for for a second
electronegative
atom.

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Acids, Bases, and the pH
Scale
 Acid:
 Molecule that can release protons (H+
).
 Proton donor.
 Base:
 Negatively charged ion that can combine
with H+
.
 Proton acceptor.

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pH
 pH = log _1__
[H+
]
 Normal pH blood = 7.35 - 7.45.
 Buffer:
 System of molecules and ions that
act to prevent changes in [H+
].

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Organic Molecules
 Molecules that contain carbon and
hydrogen.
 Carbon has 4 electrons in outer
orbital.
 Carbon covalently bonds to fill its
outer orbital with 8 electrons.

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Organic Molecules
 Organic Chemistry: deals with
molecules that contain carbon
 More than 5 million organic compounds
have been identified
 The carbon atom can form bonds with a
greater number of different elements
than any other type of atom

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Functional Groups
 Inactive “backbone” to which more
reactive atoms are attached.

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Classes According to
Functional Groups
 Ketone and
aldehyde:
carbonyl group
 Organic acid:
carboxyl group
 Alcohol: hydroxyl
group

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Stereoisomers
 Exactly the same atoms arranged in
same sequence.
 Differ in spatial orientation of a
functional group.
 D-isomers: right-handed
 L-isomers: left-handed
 Enzymes of all cells can combine only
with the L-amino acids and
D-sugars.

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Four main classes of
Organic molecules
 Lipids
 Carbohydrates
 Proteins
 Nucleic Acids

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Lipids
 GR: Lipos=Fat
 Diverse group of molecules.
 Insoluble in polar solvents (H20).
 Hydrophobic (nonpolar)
 Consist primarily of hydrocarbon
chains and rings.

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Lipids
 Hydrocarbons
 Fatty acids
 Triglycerides
 Ketone Bodies
 Phospholipids
 Steroids
 Prostaglandins

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Hydrocarbons
 Includes oils and
gases
 Carbons can be
single bonds
(saturated)
 Carbons can be
double bonded
(unsaturated)

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Fatty acids
 Nonpolar hydrocarbon chain
 Can be saturated (are stright)
 Can be unsaturated (bend at the double
bond)
 Can be poly unsaturated (multiple bends)
 Carboxyl group on one end
 Large group

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Triglycerides
 Formed by condensation of glycerol and 3
fatty acids.
 Ester bond
 Fatty acid consists of hydrocarbon chain with
carboxylic acid end.
 May be saturated or unsaturated
 Saturated fats:

Mostly animal sources

Mostly solid at room temperature
 Unsaturated fats

Mostly plant sources

Mostly liquid at room temperature

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Nutritional considerations
of triglycerides
 Also called fat or neutral fat
 Stored in adipose cells
 Total fat intake should be about 30% of
total energy intake
 Saturated fat >10%
 Saturated fats are implicated in heart
disease and stroke
 Data suggests they promote high blood
cholesterol

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Phospholipids
 A number of categories
 All contain a phosphate group
 Most common
 Glycerol (3 carbons)
 Fatty Acids on carbon 1 and 2
 Phosphate group attached to carbon (and
other polar groups eg.: choline)

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Lecithin

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Phospholipid
 Are amphipathic: contain both polar and
nonpolar domains
 Head:

contains polar groups

Hydrophilic
 Tail:

Contains fatty acids (nonpolar)

Hydrophobic

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Phospholipids
 Major component of cell membranes
 Hydrophylic heads orient to water
 Hydrophobic tails orient to each other
 Kind of phospholipid varies based on
cell or organelle

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Micelle formation

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Ketone Bodies
 Results from the hydrolysis of
triglycerides by adipocytes
 Liberates free FA into blood
 FA function as an acid in blood
 Most FA used as energy source by
some tissues
 If not, converted by liver into Ketone
bodies

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Ketone Bodies
4-carbon chunks

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Ketone Bodies
 Produced in the rapid breakdown of FA
 Low-carbohydrate diets
 Uncontrolled Diabetes mellitus
 Ketosis: Elevated level of FA in blood
 Ketoacidosis: ketosis is high enough to
lower blood ph

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Steroids
 Nonpolar and insoluble in H20.
 All have cholesterol as precursor.

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Prostaglandins
 Prostaglandins:
 Fatty acid with cyclic hydrocarbon
group.
 Derived from arachidonic acid.

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Prostaglandins

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Carbohydrates
 Organic molecules that contain
carbon, hydrogen and oxygen.
 CH20
 General formula:
 CnH2nOn
 -ose denotes a sugar molecule

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Carbohydrates
 Supply energy
 Glucose
 Complex carbohydrates
 Provide structural support
 cellulose
 Part of plasma membrane
 Monomer: monosaccarides

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Carbohydrates
 Monosaccharide: the “simple sugars”
 Pentoses (5-carbons):

Ribose: in RNA

Deoxyribose: in DNA
 Hexoses (6-carbons):structural isomers

Glucose, fructose and galactose

Characteristics
 Soluable
 Sweet
 Alcoholic fermentation

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Glucose
 Also called :
 Dextrose
 Transportable in the blood

Blood glucose
 C6H12O6

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Fructose
 Fruit sugar

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Galactose
 C6H12O6

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Carbohydrates
 Disaccharide:
 2 monosaccharides joined covalently.

Sucrose
 Glucose and fructose

Maltose
 Glucose and glucose

Lactose
 Glucose and galactose

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Disaccharides
 Characteristics
 Sweet
 Soluable
 Can be fermented
 Formation: called condensation
 Requires an enzyme
 Removal of molecule of water
 Also called dehydration synthesis
 Formation of a covalent bond

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Formation of Disaccharides

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Hydrolysis
 Reverse of dehydration synthesis.
 Digestion reaction.
 H20 molecule split.

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Carbohydrates
 Polysaccharides:
 Many monosaccharides joined covalently.
 General formula: (C6H10O5)n
 Characteristics:

Devoid of taste

Do not form solutions

Iodine test
 Iodine +starch+blue

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Polysaccarides
 Kinds:
 Starch

Glucose subunits

branched
 Dextrins
 Glycogen (animal starch)

Glucose subunits

Branched
 Cellulose

Glucose subunits

Long, unbranched chains

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Proteins
 General Information:
 GR: proteios=first rank
 ~50% of the organic material of the
body
 Functions

Structural:
 Cell structures, CTs

Functional:
 Enzymes, hormones, Hb, etc!

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Proteins
 Protein Structure
 Large molecules (polymers)
composed of amino acid sub-units
(monomers).
 Amino Acid structure
 amino group (NH2)

carboxylic acid group (COOH)

Radical group (R): functional group

H

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Proteins
 20 different standard amino acids.
 Based on the properties of the
functional group
 E.g.:

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Proteins
 Dehydration synthesis:
 Amino end of one amino acid
combines with hydroxyl group of
carboxylic end of another amino acid.
 Peptide bond:
 Bond between two adjacent amino
acids.

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Peptide bond

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Proteins
 Dipeptide: 2 amino acids
 Tripeptide: 3 amino acids
 Polypeptide: many amino acids
 Number of amino acids varies
 Up to 100 aa
 Protein
 Over 100aa
 Great variety!

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Protein structure
 Four structural levels
 Primary structure

Based on amino acid sequence

Amino acid sequence determined by DNA
 Secondary structure

Based on hydrogen bonding between close aa
 Tertiery structure

3-D shape
 Quaternary structure

Only in proteins with 2 or more polypeptide
chains

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Secondary structure (2o
)
 Based on the primary structure
 Weak hydrogen bonds form between
hydrogen and oxygen of a different amino
acid.
 Two main kinds of secondary structure:
 Alpha helix: Bond cause chain to twist in a helix.
 Beta pleated sheet: interactions between lengths
of the polypeptide chain

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Secondary structures

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Tertitary structure
 Polypeptide chains bend and fold.
 Based on interactions with aa in different parts of
the polypeptide chain

disulfide bonds: covalent

Hydrogen bonds: weak
 Produce 3 -dimensional shapes.
 Chemical interaction of each protein produces
own characteristic tertiary structure
 Denaturing protein
 Irreversible disruption of tertiary structure

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Bonds responsible for 3o
structure

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Tertiary structure

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Quaternary Structure
 Number of
polypeptide
chains
covalently
linked
together.
 Insulin,
hemoglobin

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Conjugated proteins
 Protein combined with another type of
molecule
 Glycoproteins: carbohydrate with protein
 Membranes, hormone
 Lipoproteins: Lipid and protein
 Membranes, blood plasma
 Hemoproteins: iron and protein
 Hemoglobin, cytochromes

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Nucleic Acids
 Include the macromolecules:
 DNA: deoxyribonucleic acid
 RNA: ribonucleic acid
 Involved in heredity and genetic regulation
 Are polymers:
 Monomeric subunit:nucleotides
 Bonded together in a dehydration synthesis
reaction

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Nucleic Acids

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Nucleotides
 Structure of a nucleotide: 3 subunits
 Pentose sugar
 Phosphate group
 Nitrogenous base

Purines: two rings
 Guanine
 Adenine

Pyrimidines: one ring
 Cytosine
 Thymine
 Uricil

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Nucleotide Structure

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Nitrogenous Bases

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DNA
 Huge molecules with simple structure
 Big time data storage!
 Structure
 Nucleotides

Pentose sugar: Deoxyribose

Bases:
 Purines: G and A
 Pyrimidines: C and T
 Form double-stranded helix

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DNA
 Nucleotide strands: 2
 Sugar-phosphate backbone
 Bases stick out
 Bases bond to each other
 Base pairing:
 A – T
 G – C
 Called law of complementary base pairing

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Nitrogenous Bases

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DNA

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RNA
 Means by which DNA directs cellular activities
 Structure
 Pentose sugar: ribose
 Bases: uracil (not thymine)
 Single stranded
 Three main types
 Messenger RNA (mRNA)
 Transfer RNA (tRNA)
 Ribosomal RNA (rRNA)

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DNA vs RNA