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A review of the structure and function of a living cell:
Computer scientists and
Biologists collaborated, using
the latest scientific data, to put
together a movie of the inside
of a living cell:
http://www.studiodaily.com/main/technique/tprojects/6850.html
OK, now that we know the structures
and functions inside different types of
cells, now we need to know:
What makes up those cellular
structures??
Carbohydrates, lipids,
proteins, and nucleic acids… all
surrounded by water!
Before we can understand
how these molecules work
together to build a cell, we
need to understand some
basic chemistry…
Chapter 2
Essential Chemistry for Biology
The Flow of Matter…
Wait a minute,
WHAT is MATTER?
– Matter is anything that occupies space and has
mass.
– Matter is found on the Earth in three physical
states:
•Solid
•Liquid
•Gas
– Matter is composed of
chemical elements.
• There are 92 naturally
occurring elements on Earth.
– All the elements are listed in
the periodic table.
Twenty-five elements are
essential to life
• Four of these make up about 96% of the weight
of the human body.
• Trace elements occur in smaller amounts.
Check out:
http://www.chem4kids.com/files/atom_intro.html
Each Element consists of one type of Atom
– Atoms are composed of subatomic
particles.
• A proton is positively charged.
• An electron is negatively charged.
• A neutron is electrically neutral.
Example:
a helium atom
Electron Arrangement and the
Chemical Properties of Atoms
– Electrons determine how an atom behaves
when it encounters other atoms.
Copyright © 2007 Pearson Education Inc., publishing as Pearson Benjamin Cummings
–Electrons orbit the nucleus of an atom in specific
electron shells.
•The number of electrons in the outermost shell
determines the chemical properties of an atom.
Chemical Bonds
– Chemical reactions enable atoms to give up or
acquire electrons in order to complete their outer
shells.
• These interactions usually result in atoms staying
close together.
• The atoms are held together by chemical bonds.
– Three main types of chemical bonds:
• Ionic bonds
• Covalent bonds
• Hydrogen bonds
Stronger bonds
Weaker bonds
Ionic Bonds
– When an atom loses or gains electrons,
it becomes electrically charged.
• Charged atoms are called ions.
• Ionic bonds are formed between oppositely
charged ions.
Covalent Bonds
– A covalent bond forms when two atoms
share one or more pairs of outer-shell
electrons.
What happens when the electrons in a
covalent bond are shared unequally?
– Water is a compound in which the
electrons in its covalent bonds are
shared unequally.
• Oxygen is greedy for electrons and keeps
their negative charge closer to itself.
• This causes it to be a polar molecule, one with
opposite charges on opposite ends.
+
-
Covalent
bonds where
electrons are
shared
unequally
Hydrogen Bonds
– The polarity of
water results in
weak electrical
attractions
between
neighboring water
molecules called
hydrogen bonds.
Covalent bond
with unequally
shared electrons
Chemical Reactions
– Cells constantly rearrange molecules by
breaking and forming chemical bonds.
• These processes are called chemical reactions.
– Chemical reactions cannot create or destroy
matter,
• They only rearrange it.
Water and Life
– Life on Earth began in water and evolved there
for 3 billion years.
• Modern life still remains tied to water.
• Your cells are composed of 70%–95% water.
– The abundance of water is a major reason Earth
is habitable.
Water’s Life-Supporting
Properties
– The polarity of water molecules and the
hydrogen bonding that results explain most of
water’s life-supporting properties:
•
•
•
•
Water’s cohesive nature
Water’s ability to moderate temperature
Floating ice
Versatility of water as a solvent
The Cohesion of
Water
– Water molecules stick together
as a result of hydrogen bonding.
• This is called cohesion.
• 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.
• Hydrogen bonds give water an unusually high
surface tension due to cohesion.
How Water Moderates
Temperature
– Because of hydrogen bonding, water has a
strong resistance to temperature change.
– Heat and temperature are related, but different.
• Heat is an amount of energy. This energy causes
movement of atoms and molecules.
• Temperature measures this movement of the atoms
and molecules.
http://sv.berkeley.edu/chemicalinteractions/menu.html
– Water can absorb and store large amounts of
heat while only changing a few degrees in
temperature.
– Water can moderate temperatures.
• Earth’s giant water supply causes temperatures
to stay within limits that permit life.
• Evaporative cooling removes heat from the
Earth and from organisms.
The Biological Significance of
Ice Floating
– When water molecules get cold, they move
apart, forming ice.
• A chunk of ice has fewer molecules than an equal
volume of liquid water.
– The density of ice is lower than liquid water.
Ice
Floats!
– Since ice floats, ponds, lakes, and even
the oceans do not freeze solid.
• Marine life could not survive if bodies of water
froze solid.
http://majorlycool.com/category/animals/blogid/1
Water as the Solvent of Life
– 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.
An aqueous solution
The slight negative charge of the oxygen in a water molecule
attracts it to the positive charge of the Na+ ion.
The slight positive charge of the hydrogen atoms in a water
molecule attracts them to the negative charge of the Cl- ion.
As the water molecules surround the ions of NaCl they become
dissolved in the water!
An aqueous solution
A Group Challenge:
• Based on the information of how NaCl
becomes dissolved in water, can you
figure out:
– Why carbohydrates, proteins, and nucleic
acids can dissolve in water?
– Why lipids (fats and oils) cannot dissolve in
water?
Acids, Bases, and
pH
– Acid
• A chemical
compound that
donates H+ ions to
solutions.
– Base
• A compound that
accepts H+ ions
and removes them
from solution.
Chapter 3
The Molecules of Life
Organic Molecules
– A cell is mostly water.
• The rest of the cell consists mostly of carbonbased molecules called organic molecules.
Carbon Chemistry
– Carbon is a versatile atom.
• It has four electrons in an outer shell
that holds eight.
• Carbon can share its electrons with other
atoms to form up to four covalent bonds.
Shape defines function!
– Each type of organic molecule has a
unique three-dimensional shape that
defines its function in an organism.
• The molecules of your body recognize one
another based on their shapes.
Giant Molecules from Smaller
Building Blocks
– On a molecular scale, many of life’s
molecules are gigantic.
• Biologists call them macromolecules.
• Examples: DNA, carbohydrates, proteins
– Most macromolecules are polymers.
• Polymers are made by stringing together many
smaller molecules called monomers.
• Cells link monomers by dehydration reactions.
Monomer - means “one” unit
Monomer - means “one” unit
Dimer - means “two” units
Monomer - means “one” unit
Dimer - means “two” units
Polymer - means “many” units
– Organisms also have to break down
macromolecules.
• Cells do this by a process called hydrolysis.
Monomer - means “one” unit
Dimer - means “two” units
Polymer - means “many” units
Monomer - means “one” unit
Dimer - means “two” units
Monomer - means “one” unit
Biological Molecules
– There are four categories of large molecules in
cells:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
Biological Molecules
– There are four categories of large molecules in
cells:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
Biological Molecules
– There are four categories of large molecules in
short
cells:
sugar
molecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
L-O-N-G
starch
molecules
Monosaccharides
short
sugar
molecules
– Monosaccharides are simple sugars.
• Glucose is found in sports drinks.
• Fructose is found in fruit.
Monomer - means “one” unit
Monosaccharides
are the main fuel
that cells use to do
work.
Abbreviated
structure
OR
Disaccharides
– A disaccharide is a double sugar.
• It is constructed from two monosaccharides.
– Disaccharides are joined through a
dehydration reaction.
Monomer - means “one” unit
Dimer - means “two” units
– Lactose is another type of disaccharide.
• Some people have trouble digesting lactose, a
condition called lactose intolerance.
– The most common disaccharide is sucrose,
common table sugar.
• It consists of a glucose linked to a fructose.
• Sucrose is extracted from sugar cane and the roots of
sugar beets.
– The United States is one of the world’s leading
markets for sweeteners.
• The average American consumes about 64 kg of
sugar per year.
Polysaccharides
Monomer - means “one” unit
Dimer - means “two” units
Polymer - means “many” units
– Complex
carbohydrates
are called
polysaccharides.
• They are long
chains of sugar
units.
• They are
polymers of
monosaccharides
.
Remember this??
An aqueous solution
– Simple sugars and double sugars dissolve
readily in water.
• They are hydrophilic, or “water-loving.”
Slight negative
charge of oxygen in
water and sugar
molecules
are attracted to
Slight positive
charges of
hydrogen in water
and sugar
molecules.
Abbreviated
structure
OR
I Love
You!
Where are carbohydrates in a
cell?
In the cell wall as cellulose
In the cytosol as an energy source
In amyloplasts in
plants as starch
(organelle not shown)
Biological Molecules
– There are four categories of large molecules in
small
cells:
sugar
molecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
L-O-N-G
starch
molecules
Biological Molecules
– There are four categories of large molecules in
cells:
–fats
• Carbohydrates
• Lipids
–steroids
• Proteins
• Nucleic acids
–Lipids are hydrophobic.
•They do not mix with water
Fats
Functions: energy storage, cushioning, insulation
Fats are formed by linking fatty acids onto a glycerol
molecule by dehydration reactions
– Dietary fat consists largely of the molecule
triglyceride.
Run
Away!
• Triglyceride is a combination of glycerol and
three fatty acids.
No charge! Cannot interact with water!
(hydrophobic)
– Unsaturated fats
• Have less than the maximum number of hydrogens
bonded to the carbons. (double and triple bonds)
– Saturated fats
• Have the maximum number of hydrogens bonded to
the carbons. (all single bonds)
Saturated Fatty Acids:
Too much of a good thing can be bad
– Most animal fats have a high proportion of
saturated fatty acids, which can be unhealthy.
• Example: butter
– Most plant oils tend to be low in saturated fatty
acids.
• Example: corn oil
WHY are too many saturated fats unhealthy?
– Not all fats are unhealthy.
• Some fats perform important functions in the
body and are essential to a healthy diet.
Special Lipid: Phospholipids
• Phospholipids form a two-layered
membrane, the phospholipid bilayer.
Negative charge interacts with water!
(hydrophilic)
No charge!
Cannot
interact with
water!
(hydrophobic)
Water!
Other Lipids: Steroids
– Steroids are very different from fats in structure
and function.
• The carbon skeleton is bent to form four fused rings.
– Cholesterol is the “base steroid” from which your
body produces other steroids.
• Example: sex hormones
Cholesterol is a key component
of cellular membranes…
– Synthetic anabolic steroids are
controversial.
• They are variants of testosterone.
Where are lipids in a cell?
In the smooth ER where lipids are synthesized
In the all membranes as phospholipids
Triglycerides (Ex: fat in animal cells, seed oils in
plant cells) stored in cytoplasm (not shown)
Biological Molecules
– There are four categories of large molecules in
cells:
–fats
• Carbohydrates
• Lipids
–steroids
• Proteins
• Nucleic acids
–Lipids are hydrophobic.
•They do not mix with water
Biological Molecules
– There are four categories of large molecules in
cells:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
Proteins
– A protein is a polymer constructed from
amino acid monomers.
– Proteins perform most of the tasks the
body needs to function.
Structural Proteins
Receptor Proteins
Storage Proteins
Enzymes
Contractile Proteins
Hormonal Proteins
Transport Proteins
Sensory Proteins
Defensive Proteins
Gene Regulatory
Proteins
Structure of an
Amino Acid
Structure of an
Amino Acid
Run
Away!
I Love
You!
The
Monomers:
Amino Acids
– All proteins are
constructed from
a common set of
20 kinds of
amino acids.
– Some fear water
(hydrophobic)
– Some love water
(hydrophilic)
Structure gives
Function!
Proteins as Polymers
– Cells link amino
acids together by
dehydration
reactions.
• The resulting
covalent bond
between them is
called a peptide
bond.
– Your body has tens of thousands of
different kinds of protein.
• The arrangement of amino acids makes each
one different.
Structure gives Function!!
Protein Shape
– Proteins have four levels of structure.
•
•
•
•
Primary
Secondary
Tertiary
Quaternary
1st level
2nd level
3rd level
4th level
– Primary structure
• The specific sequence of amino acids in a
protein
– A slight change in the primary structure of
a protein affects its ability to function.
• The substitution of one amino acid for another
in hemoglobin causes sickle-cell disease.
Protein
Shape
– Primary
structure
held together
by covalent
bonds
– Secondary
structure
held together
by hydrogen
bonds
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 happens by disrupting the hydrogen bonds
that hold together the shape of a protein.
– This is called denaturation.
– If the shape unfolds, the function is destroyed…
The Plasma Membrane:
A Fluid Mosaic of Lipids and
Proteins
– The membranes of cells are composed
mostly of:
• Lipids
• Proteins
Copyright © 2007 Pearson Education, Inc. publishing as Pearson Benjamin Cummings
– The lipids belong to a special category
called phospholipids.
– Phospholipids form a two-layered
membrane, the phospholipid bilayer.
– Most membranes have specific proteins
embedded in the phospholipid bilayer.
Membrane phospholipids and
proteins can drift about in the plane
of the membrane
– This behavior leads to the
description of a membrane
as a fluid mosaic:
• Molecules can move freely
within the membrane.
• A diversity of proteins exists
within the membrane.
Where are proteins in a cell?
Everywhere!! Proteins are enzymes, and structural, transport,
receptor, regulatory, contractile proteins, etc, and perform
most of the functions of a cell!
In the all membranes as integral membrane proteins
Biological Molecules
– There are four categories of large molecules in
cells:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
Biological Molecules
– There are four categories of large molecules in
cells:
• Carbohydrates
DNA, deoxyribonucleic acid
• Lipids
• Proteins
• Nucleic acids
RNA, ribonucleic acid
Nucleic Acids
– Nucleic acids are information storage
molecules.
• They provide the directions for building
proteins.
Transcription
Translation
– Nucleic acids are polymers of nucleotides.
I Love
You!
Nucleic acids
are hydrophilic!
– Each DNA nucleotide has one of the following
bases:
– Nucleotide
monomers are
linked into long
chains.
• These chains are
called
polynucleotides, or
DNA strands.
• A sugar-phosphate
backbone joins them
together.
– Two strands of DNA
join together to form a
double helix.
– RNA, ribonucleic acid, is different from
DNA.
• Its sugar has an extra OH group.
• It has the base uracil (U) instead of thymine (T).
Where are nucleic acids in a cell?
DNA is in the nucleus, mitochondria, and chloroplasts
RNA is in the nucleus, mitochondria, chloroplasts,
cytosol, and ribosomes!