Download Hydrogen bonds

Chapter 2
• Key Concepts
• 2.1 Atomic Structure Is the Basis for Life’s
Chemistry
• 2.2 Atoms Interact and Form Molecules
• 2.3 Carbohydrates Consist of Sugar Molecules
• 2.4 Lipids Are Hydrophobic Molecules
• 2.5 Biochemical Changes Involve Energy
Why is the search for water important in
the search for life?
• Living and nonliving matter is composed of
atoms.
• Like charges repel; different charges attract.
• Most atoms are neutral because the number
of electrons equals the number of protons.
• Dalton—mass of one proton or neutron
•
(1.7 × 10–24 grams)
• Mass of electrons is so tiny, it is usually
ignored.
• Element—pure substance that contains
only one kind of atom
• Living things are mostly composed of six
elements:
• Carbon (C) Hydrogen (H)
Nitrogen
(N)
• Oxygen (O) Phosphorus (P) Sulfur (S)
• The number of protons identifies an element.
• Number of protons = atomic number
• For electrical neutrality:
protons = electrons
• Mass number is the number of protons plus
neutrons
• Bohr model for atomic structure: atom is
largely empty space; the electrons occur in
orbits, or electron shells.
• Bohr models are simplified, but useful in
understanding how atoms behave.
• Behavior of electrons determines whether a
chemical bond will form between atoms and
what shape the bond will have.
• Octet rule: for elements 6–20, an atom will
lose, gain, or share electrons in order to
achieve a stable configuration of 8 electrons in
its outermost shell.
• When atoms share electrons, they form stable
associations called molecules.
• A chemical bond is an attractive force that
links atoms together in molecules.
• There are several kinds of chemical bonds.
• Covalent bonds form when two atoms share
pairs of electrons.
• The atoms attain stability by having full outer
shells.
• Each atom contributes one member of the
electron pair.
• Carbon atoms have 6 electrons; 4 in the outer
shell.
• They can form covalent bonds with four other
atoms.
• Properties of molecules are influenced by
characteristics of the covalent bonds:
– Orientation—length, angle, and direction of bonds
between any two elements are always the same.
Example: Methane always
forms a tetrahedron.
– Strength and stability—covalent bonds are very
strong; it takes a lot of energy to break them.
– Multiple bonds
Single—sharing 1 pair of electrons
C H
Double—sharing 2 pairs of electrons
C C
Triple—sharing 3 pairs of electrons
N N
• Two atoms of different elements do not
always share electrons equally.
• The nucleus of one element may have greater
electronegativity—the attractive force that an
atomic nucleus exerts on electrons.
•
Depends on the number of protons and
the distance between the nucleus and
electrons.
• If atoms have similar electronegativities, they
share electrons equally (nonpolar covalent
bond).
• If atoms have different electronegativities,
electrons tend to be near the most attractive
atom, forming a polar covalent bond.
• The partial charges that result from polar
covalent bonds produce polar molecules or
polar regions of large molecules.
• Polar bonds influence interactions with other
molecules.
• Polarity of water molecules determines many
of water’s unique properties.
• Hydrogen bonds:
• Attraction between the δ– end of one
molecule and the δ+ hydrogen end of another
molecule.
•
They form between water molecules and
within larger molecules.
• Although much weaker than covalent bonds,
they are important in the structure of DNA
and proteins.
• Hydrogen bonding contributes to properties of
water that are significant for life:
– Water is a solvent in living systems—a liquid in
which other molecules dissolve.
– Water molecules form multiple hydrogen bonds
with each other—this contributes to high heat
capacity.
• A lot of heat energy is required to raise the
temperature of water—the heat energy
breaks the hydrogen bonds.
• In organisms, presence of water shields them
from fluctuations in environmental
temperature.
– Water has a high heat of vaporization: a lot of
heat energy is required to change water from the
liquid to gaseous state (to break the hydrogen
bonds).
• Thus, evaporation has a cooling effect on the
environment.
• Sweating cools the body—as sweat evaporates from
the skin, it absorbs some of the adjacent body heat.
– Hydrogen bonds give water cohesive strength, or
cohesion—water molecules resist coming apart
when placed under tension.
– Hydrogen bonding between liquid water
molecules and solid surfaces allows for adhesion
between the water and the solid surface.
• Cohesion and adhesion allow narrow columns of water
to move from roots to the leaves of plants.
– Surface tension: water molecules at the surface
are hydrogen-bonded to other molecules below
them, making the surface difficult to puncture.
This allows spiders to walk on the surface of a
pond.
• Any polar molecule can interact with any
other polar molecule through hydrogen
bonds.
– Hydrophilic (“water-loving”): in aqueous solutions,
polar molecules become separated and
surrounded by water molecules.
• Nonpolar molecules are called hydrophobic
(“water-hating”); the interactions between
them are hydrophobic interactions.
• When one atom is much more electronegative
than the other, a complete transfer of
electrons may occur.
• This makes both atoms more stable because
their outer shells are full.
• The result is two ions—electrically charged
particles that form when atoms gain or lose
one or more electrons.
• Cations—positively charged ions
• Anions—negatively charged ions
• Ionic attractions result from the electrical
attraction between ions with opposite
charges.
The resulting molecules are called salts or
ionic compounds.
• Ionic attractions are weak, so salts dissolve
easily in water.
place text art pg 25 here
• Functional groups—small groups of atoms
with specific chemical properties
• Functional groups confer these properties to
larger molecules (e.g., polarity).
• One biological molecule may contain many
functional groups that determine molecular
shape and reactivity.
– Proteins—formed from different combinations of
20 amino acids
– Carbohydrates—formed by linking sugar
monomers (monosaccharides) to form
polysaccharides
– Nucleic acids—formed from four kinds of
nucleotide monomers
– Lipids—noncovalent forces maintain the
interactions between the lipid monomers
• Polymers are formed and broken apart in
reactions involving water.
– Condensation—removal of water links monomers
together
– Hydrolysis—addition of water breaks a polymer
into monomers
• Carbohydrates
– Source of stored energy
– Transport stored energy within organisms
– Structural molecules give many organisms their
shapes
– Recognition or signaling molecules can trigger
specific biological responses
• Monosaccharides are simple sugars.
• Pentoses are 5-carbon sugars.
• Ribose and deoxyribose are the backbones of
RNA and DNA.
• Hexoses (C6H12O6) include glucose, fructose,
mannose, and galactose.
• Monosaccharides are covalently bonded by
condensation reactions that form glycosidic
linkages to form disaccharides.
place text art pg 27 here
• Oligosaccharides contain several
monosaccharides.
– Many have additional functional groups.
– They are often bonded to proteins and lipids on
cell surfaces, where they serve as recognition
signals.
• The human blood groups (ABO) get their specificity
from oligosaccharide chains.
• Polysaccharides are large polymers; the
chains can be branching.
– Starches—polymers of glucose
– Glycogen—highly branched polymer of glucose;
main energy storage molecule in mammals
• Cellulose—the main component of plant cell
walls.
– It is the most abundant carbon-containing
(organic) biological compound on Earth.
– Very stable; good structural material
• Lipids
• Hydrocarbons (composed of C and H atoms)
that are insoluble in water because of many
nonpolar covalent bonds.
• When close together, weak but additive van
der Waals interactions hold them together.
• Lipids:
– Store energy in C—C and C—H bonds
– Play structural roles in cell membranes
– Fat in animal bodies serves as thermal insulation
• Triglycerides (simple lipids)
– Fats—solid at room temperature
– Oils—liquid at room temperature
– Have very little polarity and are extremely
hydrophobic.
• Triglycerides consist of:
– Three fatty acids—nonpolar hydrocarbon chain
attached to a polar carboxyl group (—COOH)
(carboxylic acid)
– One glycerol—an alcohol with three hydroxyl (—
OH) groups
• Synthesis of a triglyceride involves three
condensation reactions.
• The fatty acid chains can vary in length and
structure.
• In saturated fatty acids, all bonds between
carbon atoms are single; they are saturated
with hydrogens.
• In unsaturated fatty acids, hydrocarbon
chains have one or more double bonds. This
causes kinks in the chain and prevents
molecules from packing together tightly.
• Because the unsaturated fatty acids do not
pack tightly, they have low melting points and
are usually liquid at room temperature.
place text art pg 30 here
• Fatty acids are amphipathic; they have a
hydrophilic end and a hydrophobic tail.
• Phospholipid—two fatty acids and a
phosphate group bound to glycerol;
•
The phosphate group has a negative
charge, making that part of the molecule
hydrophilic.
• In an aqueous environment, phospholipids
form a bilayer.
• The nonpolar, hydrophobic “tails” pack
together and the phosphate-containing
“heads” face outward, where they interact
with water.
• Biological membranes have this kind of
phospholipid bilayer structure.
• Chemical reactions occur when atoms have
enough energy to combine or change bonding
partners.
•
sucrose + H2O
•
•
(C12H22O11)
reactants
glucose + fructose
(C6H12O6) (C6H12O6)
products
• Chemical reactions involve changes in energy.
• Energy can be defined as the capacity to do
work, or the capacity for change.
• In biochemical reactions, energy changes are
usually associated with changes in the
chemical composition and properties of
molecules.
• All forms of energy can be considered as
either:
– Potential—the energy of state or position, or
stored energy
– Kinetic—the energy of movement; the type of
energy that does work; that makes things change
• Energy can be converted from one form to
another.
• Metabolism—sum total of all chemical reactions
occurring in a biological system at a given time
• Metabolic reactions involve energy changes.
Energy is either stored in, or released from,
chemical bonds.
• A chemical reaction will occur spontaneously if
the total energy consumed by breaking bonds in
the reactants is less than the total energy
released by forming bonds in the products.
• Two basic types of metabolism:
– Anabolic reactions link simple molecules to form
complex ones.
• They require energy inputs (endergonic or
endothermic; energy is captured in the chemical bonds
that form.
– Catabolic reactions: energy is released (exergonic
or exothermic)
• Complex molecules are broken down into simpler ones.
• Energy stored in the chemical bonds is released.
• Catabolic and anabolic reactions are often
linked.
• The energy released in catabolic reactions is
often used to drive anabolic reactions—to do
biological work.
• The laws of thermodynamics apply to all
matter and energy transformations in the
universe.
– First law: Energy is neither created nor destroyed.
– Second law: Useful energy tends to decrease.
• When energy is converted from one form to
another, some of that energy becomes
unavailable for doing work.
• No physical process or chemical reaction is
100% efficient—some of the released energy
is lost in a form associated with disorder.
• This energy is so dispersed that it is unusable.
• Entropy is a measure of the disorder in a
system.
• As a result of energy transformations, disorder
tends to increase.
• If a chemical reaction increases entropy, its
products are more disordered or random than
its reactants.
• If there are fewer products than reactants, the
disorder is reduced; this requires energy to
achieve.
• Metabolism creates more disorder (more
energy is lost to entropy) than the amount of
order that is stored.
• Example:
– The anabolic reactions needed to construct 1 kg of
animal body require the catabolism of about 10 kg
of food.
• Life requires a constant input of energy to
maintain order.
• Water is essential for life. One way to investigate
the possibility of life on other planets is to study
how life may have originated on Earth.
• Experiments in the 1950s combined gases
thought to be present in Earth’s early
atmosphere, including water vapor. An electric
spark provided energy.
• Complex molecules formed, such as amino acids.
Water was essential in this experiment.