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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Chemical Bonds, 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

(–)
(+)

11p 17p 11p 17p

12n 18n 12n + 18n

Na + Cl NaCl

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Table Salt, an Ionically Bonded Molecule

Slide number: 2

11p 17p
12n 18n

Na + Cl

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Table Salt, an Ionically Bonded Molecule

Slide number: 3

11p 17p
12n 18n

Na + Cl

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Table Salt, an Ionically Bonded Molecule

Slide number: 4

11p 17p
12n 18n

Na + Cl

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Table Salt, an Ionically Bonded Molecule

Slide number: 5

11p 17p
12n 18n

Na + Cl

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Table Salt, an Ionically Bonded Molecule

Slide number: 6

(+) (–)

11p 17p
12n 18n

Na + Cl

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Table Salt, an Ionically Bonded Molecule

Slide number: 7

(+) (–)

11p 17p
12n 18n

NaCl

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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
 Can cause coma, death
 Filtered by the kidney
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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