Chemical Organization of Life
Download
Report
Transcript Chemical Organization of Life
About 25 of the 92 elements are essential to life
Carbon, hydrogen, oxygen, and nitrogen make up 96%
of living matter
Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
Trace elements are those required by an organism in
minute quantities
LE 2-3
Nitrogen deficiency
Iodine deficiency
Atoms
same number of protons
may differ in number of neutrons
Isotopes
Most isotopes are stable
some are radioactive, giving off particles and energy
Application of radioactive isotopes in biological
research:
Dating fossils
Tracing atoms through metabolic processes
Diagnosing medical disorders
LE 2-6
Cancerous
throat
tissue
Bonding
covalent bond
sharing of a pair of valence electrons by two atoms
shared electrons count as part of each atom’s valence
shell
molecule
single covalent bond (single bond)
sharing of one pair of valence electrons
double covalent bond (double bond)
sharing of two pairs of valence electrons
nonpolar covalent bond
atoms share the electron equally
polar covalent bond
one atom is more electronegative
atoms do not share the electron equally
LE 2-12
–
O
H
+
H
H2 O
+
Bonding
Ionic Bonds
transfer of an electron from atom to another
Create charged particles
Cation (+)
Anion (-)
ionic bond is an attraction between an anion and a
cation
forms ionic compounds, or salts
Ex. sodium chloride (table salt)
LE 2-13
Na
Cl
Na+
Cl–
Sodium atom
(an uncharged
atom)
Chlorine atom
(an uncharged
atom)
Sodium ion
(a cation)
Chlorine ion
(an anion)
Sodium chloride (NaCl)
Bonding
hydrogen bond
forms when a hydrogen atom covalently bonded to one
electronegative atom is also attracted to another
electronegative atom
the electronegative partners are usually oxygen or
nitrogen atoms
LE 2-15
–
+
Water
(H2O)
+
Hydrogen bond
–
Ammonia
(NH3)
+
+
+
Covalent = strongest bonds
Form most molecules that make up cells
Ionic & hydrogen = weak bonds
LE 2-UN44
Chemical reactions
Reactants
products
2 H2
O2
Reactants
2 H2O
Reaction
Products
Ex. Photosynthesis
sunlight powers the conversion of CO2 and H20 to
glucose (C6H12O6) and O2
Some chemical reactions go to completion
All reactants are converted to products
Most chemical reactions are reversible
Products of the forward reaction become reactants for
the reverse reaction
Chemical equilibrium is reached when the forward
and reverse reaction rates are equal
Water
All living organisms require water more than any other
substance
Most cells are surrounded by water, and cells themselves
are about 70-95% water
•
Four of water’s properties that facilitate an
environment for life:
Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent
hydrogen bonds hold water molecules together
Cohesion
Creates surface tension
helps the transport of water against gravity in plants
Adhesion of water to plant cell walls also helps to counter
gravity
LE 3-2
Hydrogen
bonds
LE 3-3
Water-conducting cells
100 µm
Moderation of Temperature
absorbs heat from warmer air
releases stored heat to cooler air
can absorb or release a large amount of heat with only a
slight change in its own temperature
“The solvent of life”
Solution
liquid that is a homogeneous mixture of substances
Solvent
dissolving agent of a solution
Solute
substance that is dissolved
Water is a versatile solvent due to:
its polarity
Readily forms hydrogen bonds
aqueous solution
water is solvent
hydrophilic
affinity for water
hydrophobic
does not have an affinity for water
Most biochemical reactions occur in water
Rate generally depends on concentration of reactants
A hydrogen atom in a hydrogen bond between two
water molecules can shift from one to the other:
The hydrogen atom leaves its electron behind and is
transferred as a proton, or hydrogen ion (H+)
The molecule with the extra proton is now a hydronium
ion (H3O+)
The molecule that lost the proton is now a hydroxide ion
(OH-)
Acid
substance that increases the H+ concentration of a solution
pH less than 7
Base
substance that reduces the H+ concentration of a solution
pH greater than 7
Most biological fluids have pH values in the range of 6 to 8
Cell pH is close to 7
LE 3-8
pH Scale
0
Increasingly Acidic
[H+] > [OH–]
1
Neutral
[H+] = [OH–]
Battery acid
2 Digestive (stomach)
juice, lemon juice
3 Vinegar, beer, wine,
cola
4 Tomato juice
5 Black coffee
Rainwater
6 Urine
7 Pure water
Human blood
8
Seawater
Increasingly Basic
[H+] < [OH–]
9
10
Milk of magnesia
11
Household ammonia
12
13
Household bleach
Oven cleaner
14
Acid Precipitation
rain, snow, or fog
pH lower than 5.6
caused by the mixing of different pollutants with water in the
air
can damage life in lakes and streams
Changes soil chemistry
contributing to the decline of some forests
LE 3-9
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
More
acidic
Acid
rain
Normal
rain
More
basic
Decomposition Reactions
In chemical notation:
AB
A+B
Releases covalent bond energy
Hydrolysis—Decomposition reaction with H•OH
E.g., food digestion
Synthesis Reactions
In chemical notation:
A+B
AB
Absorbs energy
Formation of new bonds
Dehydration synthesis
Removal of H•OH between molecules
Organic Compounds
Carbohydrates
sugars and the polymers of sugars
monosaccharides, or single sugars
molecular formulas that are usually multiples of CH2O
Ex. Glucose
Classified based on number of carbons
5 = pentose
6 = hexose
macromolecules = polysaccharides
Disaccharides = chain of 2
Ex . Sucrose (table sugar)
Monosaccharides
major fuel for cells
raw material for building molecules
In aqueous solutions they form rings
Form disaccharides through dehydration synthesis
LE 5-4
Linear and
ring forms
Abbreviated ring
structure
LE 5-5
Dehydration
reaction in the
synthesis of maltose
1–4
glycosidic
linkage
Glucose
Glucose
Dehydration
reaction in the
synthesis of sucrose
Maltose
1–2
glycosidic
linkage
Glucose
Fructose
Sucrose
Organic Compounds
Formation and Breakdown of Complex Sugars
Figure 2-11 (a), (b)
Polysaccharides
Ex. Starch
storage polysaccharide of plants
made of glucose monomers
surplus starch stored as granules within chloroplasts and other
plastids
Ex. Glycogen
storage polysaccharide in animals
Stored in liver and muscle cells
Ex. Cellulose
major component of the tough wall of plant cells
polymer of glucose
LE 5-7
a Glucose
a and b glucose ring structures
Starch: 1–4 linkage of a glucose monomers.
Cellulose: 1–4 linkage of b glucose monomers.
b Glucose
• Polymers with alpha glucose are helical
• Polymers with beta glucose are straight
• H atoms on one strand can bond with OH groups on other
strands
• Ex. Cellulose
• Grouped into microfibrils = strong building materials for
plants
LE 5-8
Cellulose microfibrils
in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose
molecules
b Glucose
monomer
Chitin
structural polysaccharide
found in the exoskeleton of arthropods
structural support for the cell walls of many fungi
used as surgical thread
Lipids
do not form polymers
have little or no affinity for water
Are hydrophobic
consist mostly of hydrocarbons, which form nonpolar
covalent bonds
Include fats, phospholipids, and steroids
Fats
Made up of glycerol and fatty acids
Glycerol = three-carbon alcohol with a hydroxyl group attached to
each carbon
fatty acid = carboxyl group attached to a long carbon skeleton
• separate from water
• water molecules form hydrogen bonds with each other and
exclude the fats
• three fatty acids joined to glycerol by an ester linkage =
triglyceride
Animation: Fats
LE 5-11a
Fatty acid
(palmitic acid)
Glycerol
Dehydration reaction in the synthesis of a fat
Fatty acids
vary in length
vary in number and locations of double bonds
Saturated fatty acids
Have maximum number of hydrogen atoms possible
no double bonds
Make up saturated fats
Animal fats
Solid at room temperature
Can contribute to cardiovascular disease (plaque deposits)
Unsaturated fatty acids
have one or more double bonds
Make up unsaturated fats
Plant and fish fats
Liquid at room temperatures
Called oils
fats = energy storage
LE 5-11b
Ester linkage
Fat molecule (triacylglycerol)
LE 5-12a
Stearic acid
Saturated fat and fatty acid.
LE 5-12b
Oleic acid
cis double bond
causes bending
Unsaturated fat and fatty acid.
Phospholipids
two fatty acids and a phosphate group are attached to glycerol
fatty acid tails are hydrophobic
phosphate group and its attachments form a hydrophilic head
When added to water, they self-assemble into a bilayer, with
the hydrophobic tails pointing toward the interior
Make up bilayer of cell membranes
LE 5-13
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Structural formula
Space-filling model
Phospholipid symbol
LE 5-14
Hydrophilic
head
Hydrophobic
tails
WATER
WATER
Steroids
carbon skeleton consisting of four fused rings
Ex. Cholesterol
component in animal cell membranes
High levels in the blood may contribute to cardiovascular disease
Proteins
Proteins account for more than 50% of the dry mass of
most cells
Protein functions include:
structural support
Storage
Transport
cellular communications
Movement
Defense against foreign substances
Enzymatic Proteins
acts as a catalyst
Speeds up chemical reactions
can perform their functions repeatedly
Digestive enzymes catalyze the hydrolysis of polymers in food
Suffix -ase
LE 5-16
Substrate
(sucrose)
Glucose
Enzyme
(sucrose)
Fructose
Structural Proteins
Support
Ex. Silk
Fibers in cocoons and webs
Ex. Collagen & elastin
Connective tissues in animals
Ex. Keratin
Hair, horns, feathers
Storage Proteins
Store amino acids
Ex. Ovalbumin
Egg whites
Source of amino acids for developing chick embryo
Ex. Casein
Milk protein
Source of amino acids for baby mammals
Plants have storage protein in seeds
Transport Proteins
Transport other substances
Ex. Hemoglobin
Contains iron
In vertebrate blood
Transports oxygen
Other transport proteins transport molecules across cell
membranes
Hormonal Proteins
Coordination of organisms activities
Ex. Insulin
Secreted by pancreas
Regulate concentration of glucose in blood of vertebrates
Causes cells to increase absorption of glucose
Receptor Proteins
Response of cell to chemical stimuli
Built into cell membrane
Contractile and Motor Proteins
Movement
Ex. Actin & Myosin
Movement in muscles
Other proteins allow for movement of cilia and flagella
Defense Proteins
Protection against disease
Ex. Antibodies
Amino Acids
organic molecules with carboxyl and amino groups
Amino acids differ in their properties due to differing side
chains, called R groups
Cells use 20 amino acids to make thousands of proteins
linked by peptide bonds
LE 5-UN78
a carbon
Amino
group
Carboxyl
group
Polypeptides
polymers of amino acids
range in length from a few monomers to more than a
thousand
Each has a unique linear sequence of amino acids
A protein consists of one or more polypeptides
4 levels of protein structure
primary structure
Its unique sequence of amino acids
Secondary structure,
found in most proteins
consists of coils and folds in the polypeptide chain
Tertiary structure
determined by interactions among various side chains (R groups)
Quaternary structure
results when a protein consists of multiple polypeptide chains
LE 5-20
b pleated sheet
+H N
3
Amino end
Amino acid
subunits
a helix
LE 5-20a
Amino end
Amino acid
subunits
Primary Structure
Determined by
inherited genetic
information
Carboxyl end
Secondary Structure
result from hydrogen bonds between repeating constituents
of the polypeptide backbone
alpha helix
beta pleated sheet
LE 5-20b
b pleated sheet
Amino acid
subunits
a helix
Tertiary structure
Determined by interactions between R groups
LE 5-20d
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Ionic bond
Quaternary structure
results when two or more polypeptide chains form one
macromolecule
Ex. Collagen
fibrous protein consisting of three polypeptides coiled like a rope
Ex. Hemoglobin
globular protein consisting of four polypeptides: two alpha and two beta
chains
LE 5-20e
Polypeptide
chain
b Chains
Iron
Heme
Polypeptide chain
Collagen
a Chains
Hemoglobin
Changes in protein
Can change conformation
Ex. Sickle-cell disease
an inherited blood disorder, results from a single amino acid
substitution in the protein hemoglobin
10 µm
Red blood Normal cells are
cell shape full of individual
hemoglobin
molecules, each
carrying oxygen.
10 µm
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
cell into sickle
shape.
LE 5-21b
Sickle-cell hemoglobin
Normal hemoglobin
Primary
structure
affe
Val
His
1
2
Leu
Thr
3
4
Pro
Glu
5
6
Secondary
and tertiary
structures
Function
7
b subunit
Primary
structure
Secondary
and tertiary
structures
Molecules do
not associate
with one
another; each
carries oxygen.
His
1
2
Leu
Thr
3
4
Function
Val
Glu
5
6
7
b subunit
Sickle-cell
hemoglobin
b
a
Pro
Exposed
hydrophobic
region
a
Quaternary
structure
b
Val
b
a
Quaternary Normal
hemoglobin
structure
(top view)
Glu
Molecules
interact with
one another to
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.
b
a
Protein conformation
Protein shape
Primary structure
pH
salt concentration
Temperature
loss of a protein’s native conformation is =
denaturation
A denatured protein is biologically inactive
LE 5-22
Denaturation
Normal protein
Denatured protein
Renaturation
Nucleic Acids
Genetic information
two types:
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
polymers called polynucleotides
monomers called nucleotides
nitrogenous base,
pentose sugar (either ribose or deoxyribose)
phosphate group
There are two families of nitrogenous bases:
Pyrimidines have a single six-membered ring
Purines have a six-membered ring fused to a five-
membered ring
LE 5-26b
Nitrogenous bases
Pyrimidines
Cytosine
C
Thymine (in DNA) Uracil (in RNA)
U
T
Purines
Adenine
A
Guanine
G
Pentose sugars
Deoxyribose (in DNA)
Nucleoside components
Ribose (in RNA)
DNA
provides directions for its own replication
directs synthesis of messenger RNA (mRNA)
through mRNA, controls protein synthesis
Protein synthesis occurs in ribosomes
The amino acid sequence of a polypeptide is programmed
by a unit of inheritance called a gene
Genes are made of DNA
RNA
Important in protein synthesis
3 types
Ribosomal RNA (rRNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
DNA
has two polynucleotides spiraling around an imaginary axis,
forming a double helix
the two backbones run in opposite 5´ to 3´ directions from
each other, an arrangement referred to as antiparallel
The nitrogenous bases in DNA form hydrogen bonds in a
complementary fashion:
A always with T
G always with C
LE 5-27
5 end
3 end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
5 end
New
strands
5 end
3 end
5 end
3 end