Download Chapter 2&3 Chemical Composition of the Body of the Body

Chapter 2 & 3 – Chemical
Composition of the Body
“Because living things, including humans,
are composed only of chemicals, it is
absolutely essential for a biology student
to have a basic understanding of
chemistry.”
Sylvia Mader..
Ecosystem
African savanna
Community
All organisms in savanna
Organism
Zebra
Organ system
Circulatory system
Population
Herd of zebras
Organ
Heart
Tissue
Heart muscle
tissue
Cell
Heart muscle cell
Molecule
DNA
Atom
Oxygen atom
• Matter is anything that occupies space and has mass and is
found on the Earth in three physical states
– Solid
– Liquid
– Gas
• Atoms – smallest unit of an element that can undergo a
chemical change.
• Composed of subatomic particles:
 Protons = (+ charge) found in the nucleus
 Neutrons = (no charge) found in the nucleus
 Electrons = (e-,- charge) found orbiting the nucleus in the electron
cloud
• The number of protons determines the atom’s identity, e.g.
6 P = carbon..
Nucleus
(a)
(b)
Cloud of negative
charge (2 electrons)
2
Protons
2
Neutrons
2
Electrons
• Atomic number = sum of P
• Atomic mass = sum of P and N
• The number of N and/or e- can change.
Isotope = change the number of N
Ion = change the number of e cation = positive ion (how does it become
positive?)
 anion = negative ion
negative?)
(how does it become
• The position of an atom’s e- is the
electron configuration. We will not study
configurations except for the outermost
level of e- = valence shell
• The e- found there are the valence e-.
• The valence e- are the ones involved in
ordinary chemical reactions..
First
electron shell
(can hold
2 electrons)
Outermost
electron shell
(can hold
8 electrons)
Electron
Hydrogen (H)
Atomic number = 1
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8..
• Bonding is accomplished by interactions
between two atom’s valence e-.
– If e- are shared between two atoms that
forms a covalent bond.
• Single bonds = one shared pair
• Double bonds = two shared pairs
• Triple bonds = three shared pairs
– If e- are transferred from one atom (ion) to
another that forms an ionic bond.
• Hydrogen bonds are special (polar)
covalent bonds that are very important
to biology..
Covalent Bonds
Ionic Bonds
Sodium atom (Na)
Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na) Chloride ion (Cl)
Sodium chloride (NaCl)
Covalent Animation
Ionic Animation..
• Electronegativity is the property that
describes an atom’s attraction for a
shared pair of e-.
• If two atoms with different electronegativity values share e-, i.e. form a
covalent bond, one of the atoms will have
a “larger share” of the e-.
• This produces a molecule with differently
charged ends (poles). This type of
molecule is called polar..
• Bonds formed between the hydrogen
end (+ charged) of a polar molecule
and the – end of any other polar
molecule or highly electronegative atom
(e.g. P, N, O) are called hydrogen
bonds.
• These hydrogen bonds are very
important because they alter the
physical and chemical properties of
many molecules (especially water)..
()
Hydrogen bond
()
()
()
()
()
()
(b)
()
• Molecules that are formed by polar
covalent bonds have a tendency to
break apart when the electron from the
hydrogen is transferred to the more
electronegative atom. This is called
dissociation or ionization.
• Water ionizes to form equal amounts of
hydroxyl (OH-) and hydrogen (hydronium, H+) ions..
Water’s Life-Supporting Properties
• The polarity of water molecules and the hydrogen
bonding that results explain most of water’s lifesupporting properties
a. Water’s cohesive nature
b. Water’s ability to moderate
temperature
c. Floating ice
d. Versatility of water as a solvent..
a. Water molecules
stick together as a
result of hydrogen
bonding = surface
tension
i.
Cohesion is vital for
water transport in
plants
–
Surface tension
is the measure
of how difficult it
is to stretch or
break the
surface of a
liquid..
b. Because of hydrogen bonding, water has a strong
resistance to temperature change and water can
moderate temperatures.
i. Water can absorb and store large amounts of
heat while only changing a few degrees in
temperature
– Earth’s giant water supply causes temperatures to
stay within limits that permit life
– Evaporative cooling removes heat from the Earth
and from organisms..
c. When water molecules get cold, they move apart,
forming ice
– A chunk of ice has fewer molecules than an
equal volume of liquid water
• Since ice floats, ponds, lakes, and even the oceans
do not freeze solid
• Marine life could not survive if bodies of water froze
solid..
d. A solution is a liquid consisting of two or more
substances evenly mixed
– The dissolving agent is called the solvent
– The dissolved substance is called the solute
• The polarity of water enhances its ability to act
as a solvent.
 Polar substances are attracted to the polar
water molecules and “pulled” out of
solution..
Salt crystal
Ion in solution
• An acid is a molecule that can release
protons (H+).
–Proton donor.
• A base is a molecule that can combine
with H+ and remove it from solution.
Bases are also defined as releasing OH-.
–Proton acceptor..
• pH = log _1__
[H+]
– [H+] = molar concentration of H+.
– pH inversely related to [H+].
• Because of logarithmic relationship, a
solution with 10 times [H+] of H20 has a
pH = 6; solution with 0.1 the [H+] has a
pH = 8..
Oven cleaner
Household bleach
Household ammonia
Basic
solution
Milk of magnesia
Seawater
Human blood
Pure water
Neutral
solution
Urine
Tomato juice
Grapefruit juice
Lemon juice;
gastric juice
Acidic
solution
pH scale
• A buffer is a system of molecules and ions
that act to prevent changes in [H+] and
stabilizes pH of a solution.
• In blood:
* H20 + C02
H2C03
H+ + HC03–Reaction can proceed in either direction
(depending upon the concentration of
molecules and ions)..
Organic Molecules
• Composed primarily of H, C, O, & N.
• Look at the common functional groups.
Hydroxyl group
Carbonyl group
Amino group
Carboxyl group
Found in alcohols
and sugars
Found in sugars
Found in amino acids
and urea in urine (from
protein breakdown)
Found in amino acids,
fatty acids, and some
vitamins
Carbohydrates
• Organic molecules
that contain carbon,
hydrogen and
oxygen.
– CnH2n0n.
• Monosaccharides =
simple sugars.
– Structural isomers:
• Glucose, fructose,
galactose.
Glucose
Fructose
• Disaccharide: 2 monosaccharides joined covalently.
– Sucrose (glucose and fructose), lactose (glucose and
galactose), maltose (2 glucose).
•Polysaccharide:
Numerous monosaccharides joined
covalently.
glycogen
(repeating glucose
joined that are
highly branched),
starch
(thousands of
glucose joined),
cellulose
(thousands of
glucose joined)..
Glucose
monomer
Starch granules in
potato tuber cells
(a) Starch
Glycogen
Granules
In muscle
tissue
(b) Glycogen
Cellulose fibril in
a plant cell wall
Cellulose molecules
(c) Cellulose
• Organic molecules are built by dehydration
synthesis:
C6H12O6 + C6H12O6
C12H22O11 + H2O
Glucose
Glucose
Maltose
• Organic Molecules are broken down by
hydrolysis
C12H22O11 + H2O
C6H12O6 + C6H12O6
Lipids
• Insoluble in water because of nonpolar
molecules
– Triglycerides = 3 fatty acids + glycerol
• Saturated = joined by only single bonds
• Unsaturated = joined by at least one double bond
• Hydrolysis of triglycerides in adipose tissue
releases free fatty acids.
– Free fatty acids can be converted in the liver
to ketone bodies.
– Excess ketone bodies can lower blood pH..
(b) A triglyceride
– Phospholipids = phosphate + fatty acid
• phosphate end is polar = hydrophilic
• fatty acid end is nonpolar = hydrophobic
– Steroids = aromatic rings = three 6-carbon
rings joined to a 5-carbon ring
• Steroid hormones are cholesterol derivitaves..
Cholesterol
Testosterone
A type of estrogen
Proteins
• Large molecules composed of long chains
of amino acids.
– 20 different amino acids can be used in
constructing a given protein.
– Each amino acid contains an amino group
(NH2) at one end and carboxyl group (COOH)
at the other end.
• Differences between amino acids are due
to differences in functional groups (“R”).
• Amino acids are joined by peptide bonds..
Amino
group
(a)
Carboxyl
group
Side
group
Side
groups
Leucine
(hydrophobic)
Serine
(hydrophobic)
• The four types of proteins
(d) Transport
proteins
(b) Storage
proteins
(a) Structural proteins
(c) Contractile proteins
Protein Structure Levels
• Primary structure is the sequence of the
amino acids in the protein.
• Secondary structure is produced by
weak hydrogen bonds between
hydrogen of one amino acid and the
and oxygen of a different amino acid
nearby.
 a-helix or b-sheet..
• Tertiary structure is formed when
polypeptide chains bend and fold to
produce 3 -dimensional shape.
– Formed and stabilized by weak chemical
bonds between functional groups.
• Each type of protein has its own own
characteristic tertiary structure.
• Quaternary structure is produced when
a number of polypeptide chains
covalently linked together..
Hydrogen bond
Pleated sheet
Polypeptide
(single subunit)
Amino acid
(a) Primary structure
Complete
protein,
with four
polypeptide
subunits
Hydrogen bond
Alpha helix
(b) Secondary
structure
(c) Tertiary
structure
(d) Quaternary structure
• A protein’s shape is sensitive to the surrounding
environment
– Unfavorable temperature and pH changes can cause a protein to
unravel and lose its shape
– This is called denaturation..
Nucleic Acids
• Include DNA and RNA.
• Nucleic acids are composed of
nucleotides to form long polynucleotide
chains.
– Each nucleotide is composed of 3 smaller
units:
• 5-carbon sugar (deoxyribose or ribose).
• Phosphate group attached to one end of sugar.
• Nitrogenous base attached to other end of
sugar..
Nitrogenous base
(A,G,C, or T)
Thymine (T)
Phosphate
group
Sugar
(deoxyribose)
Phosphate
Base
Sugar
• The “backbone” of the nucleic acid is
formed by the sugar and phosphate
pairs.
• The “rungs” are formed by paired
nitrogenous bases.
– Nitrogenous bases complementary pair
• A + T (U)
• C + G..