Transcript Document

Molecules of Life
Sections of chapters 2, 3, 4, 5, 6, 22
Quiz II Oct. 5th
Exam II Oct. 14th
Atoms and Molecules
What are living things made of?
TRACING LIFE DOWN TO THE CHEMICAL
LEVEL
• Biology includes the study of life at many levels
• In order to better understand life, in the next slide
we’ll look at the macroscopic level, the
ecosystem, and work our way down to the
microscopic level of cells
• Cells consist of enormous numbers of chemicals
that give the cell the properties we recognize as
life
Ecosystem
(African savanna)
Community
(All the organisms in the savanna)
Organism (A Zebra)
Population
(Herd of zebras)
Organ systems
(Circulatory system)
Organs
(Heart)
Cells
(Heart muscle cell)
Tissues
(Heart muscle
tissue)
Molecules
(DNA)
Chemicals
Atoms
(Oxygen atom)
SOME BASIC CHEMISTRY
• Take any physical or biological system apart and
you eventually end up at the chemical level
Chapter 2
Molecules
• Everything in the universe is made of atoms
(Atomic theory of matter).
• Atoms can bond together to make molecules.
• Living things are made of atoms and molecules, just
like any non-living thing.
Matter: What is it?
• Matter is anything that occupies space and has mass
• Matter is found on the Earth in three physical states
– Solid
– Liquid
– Gas
• All the elements are listed in the periodic table
Atomic number
Element symbol
Mass number
Figure 2.2
• The most common elements in living things are:
– Carbon
– Hydrogen
– Phosphorous
– Nitrogen
The Structure of Atoms
• What is an atom?
• Atoms are composed of subatomic particles
– A proton is positively charged
– An electron is negatively charged
– A neutron is electrically neutral
Chemical Bonding and Molecules
• Chemical reactions enable atoms to lose, gain, or
share 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
Chemical 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
Sodium atom (Na)
Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na) Chloride ion (Cl)
Sodium chloride (NaCl)
Chemical Bonds: Covalent Bonds
• A covalent bond forms when two atoms share one
or more pairs of outer-shell electrons
Figure 2.9
The Structure of Water
• Studied in isolation, the water molecule is
deceptively simple
– Its two hydrogen atoms are joined to one oxygen
atom by single covalent bonds
H
H
O
The Structure of Water: Polarity
• But the electrons of the covalent bonds are not
shared equally between oxygen and hydrogen
– This unequal sharing makes water a polar molecule
()
()
()
()
The Structure of Water: Hydrogen Bonds
• The polarity of
water results in
weak electrical
attractions between
neighboring water
molecules
– These
interactions
are called
hydrogen
bonds
()
Hydrogen bond
()
()
()
()
()
()
()
(b)
Figure 2.11b
Water’s Life-Supporting Properties
• The polarity of water molecules and the hydrogen
bonding that results explain most of water’s lifesupporting properties
– Water’s cohesive nature
– Floating ice
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
Microscopic tubes
• 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
• 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
– This is why ice floats
Hydrogen bond
Ice
Liquid water
Stable hydrogen bonds
Hydrogen bonds
constantly break and re-form
Figure 2.15
Water as the Solvent of Life
• Table salt, NaCl, is the result of an ionic bond
between Na+ and Cl- ions.
• When salt mixes with water, this ionic bond breaks,
and the separated Na+ and Cl- ions are attracted to
the polar water molecules.
Ion in solution
Salt crystal
• Elements in the Human Body
– Four elements make
up about 96% of the
weight of the human
body....
– Oxygen, Carbon,
Hydrogen, Nitrogen
– Trace elements
occur in smaller
amounts
Molecules: what are living things made of?
Chapter 3
What is the main element that
living things are made of?
Carbon Chemistry
An atom of C
– Has four electrons in an outer shell (can hold eight)
– Carbon can share its electrons with other atoms to
form up to four covalent bonds
• Carbon can use its
bonds to
Carbon skeletons vary in length
– Attach to other carbons
– Form an endless
diversity of carbon
skeletons
Carbon skeletons may be unbranched or branched
Carbon skeletons may have double bonds,
which can vary in location
Figure 3.2
Carbon skeletons may be arranged in rings
• The simplest organic compounds are
hydrocarbons
– These are organic molecules containing only carbon
and hydrogen atoms
– The simplest hydrocarbon is methane
Structural
formula
Ball-and-stick
model
Space-filling
model
Figure 3.3
• Larger hydrocarbons
– Are the main
molecules in the
gasoline we burn
in our cars
– The hydrocarbons
of fat molecules
provide energy
for our bodies
Figure 3.4
Molecules
• Most molecules in living things are polymers
• What type of reaction creates polymers of sugars?
• What type creates polymers of amino acids?
• What is the name of the reaction that breaks polymers
into monomers?
Molecules
• There are 4 classes of compounds that are the
building blocks of cells
– Carbohydrates
– Lipids (fats and oils)
– Proteins
– Nucleic acids
Carbohydrates
• Repeating subunit is
H–C–O–H
which is CH2O.
• Hence carbo-hydrate
• Can occur as ring or chain
• Monosaccharides include
simple sugars like glucose and
fructose
Carbohydrates
• Repeating subunit is
H–C–O–H
which is CH2O.
Polysaccharides
• Starch: long-term energy
storage in plants
• Hence carbo-hydrate
• Glycogen: short-term energy
storage in animals
• Can occur as ring or chain
• Cellulose: structure in plants
• Monosaccharides include
simple sugars like glucose and
fructose
• Chitin: structure in animals
• Disaccharides (sucrose,
maltose, lactose).
• Polysaccharides
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
Figure 3.13
Carbohydrates
• Carbohydrates are polar, that
is, they have an uneven charge
distribution across molecule.
Makes them soluble in water
(hydrophilic).
• Diet: No carbohydrates are
essential (you can create them
in your body from other
compounds you eat.)
• Energy density: 4 Cal/g.
Lipids
(Fats and oils)
• 4 types
– Fatty acids
–Triglycerides
–Phospholipids
–Steroids
Lipids (fats, oils, waxes)
• The repeating subunit of a
lipid is CH2:
H–C–H
• Called hydrocarbons
because they are composed
of mostly C and H.
• Lipids are nonpolar and
are thus hydrophobic.
• Energy density: 9 Cal/g,
because in carbohydrates,
the O adds mass and
removes high energy
bonds.
Fatty Acids
Fatty Acids
• Fatty acids are used for energy, or stored
• Store a lot of energy. Why?
• Evolutionary Theory can provide a plausible
explanation for why we crave fats.
Saturated fats
• Saturated fats are molecules in
which the C atoms are
saturated with H’s.
• Because the hydrocarbon chains
line up uniformly, saturated fats
are solid at room temperature
(and gummy in your arteries).
• If there were any C=C (carboncarbon double bond), it would
be unsaturated.
Unsaturated fats
• Unsaturated fats are liquid
at room temperature.
• Monounsaturated fats
(such as olive oil) are
GOOD for you, as they
reduce LDL (details to
follow).
Trans fats
• Partially hydrogenated oils (i.e.,
trans fats) are just as bad as
saturated fats (if not worse)!
• Start with a perfectly healthy
vegetable oil and hydrogenate it
(i.e., force H’s on it), making a
new type of saturated fat.
• Crisco shortening was
previously soybean oil.
Lipids
Lipids are stored primarily as triglycerides: three fatty
acids attached to a small glycerol molecule.
Creating triglycerides
?
• When 3 fatty acids are joined to a glycerol molecule, this
reaction is called ______ and produces ______.
Lipids in membranes
• Membranes are composed
primarily of phospholipids.
• Glycerol attached to 2 fatty acids
and a polar phosphate group.
• Phosphate is hydrophilic while 2
hydrocarbon chains are
hydrophobic.
• Thus they form bilayers in cells,
as the hydrocarbons avoid water
while the phosphate heads turn
towards water…
http://telstar.ote.cmu.edu/biology/downloads/membranes/index.html
Lipids: Steroids
Interconnected rings of
carbon atoms
Small molecule, but big effects
Cholesterol is another example
of a steroid
Lipids as messengers
• Lipids can act as messengers in
the body.
• These steroid hormones are ring
structures.
• Hormones send long sustained
messages, regulating slow
transitions (as opposed to fast
nervous system)
• Ex. Puberty
• Cholesterol is important in
membranes (to maintain
stability)
Testosterone
Proteins
• Composed of C, H, O, and N.
• The repeating subunit is an
amino acid.
• Central C is attached to
– amine group
– carboxyl group (acid)
– H atom
– R-group (varies
depending on amino acid)
Peptide bonds
• When 2 amino acids are joined,
the N from one’s amino group
attaches to the C of the other’s
carboxyl group.
• Forms a peptide bond.
• What is this process called?
• What is released?
• To join 3 amino acids, how
many water are released?
• When many amino acids are
joined in a chain, a protein
(polypeptide) is formed.
• Your body has tens of thousands of different kinds
of proteins
• Proteins do many different jobs, some are
hormones, some are enzymes, some are structural
• The arrangement of amino acids makes each one
different, differently shaped proteins have different
functions.
• Primary structure
5
1
30
35
– The specific
sequence of
amino acids in a
protein
15
10
20
25
45
40
50
55
65
60
70
85
80
75
95
90
100
110
105
115
120
125
129
Figure 3.21
Amino acid
• 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
1
2
(b) Sickled red blood cell
6
7. . . 146
4
5
Normal hemoglobin
(a) Normal red blood cell
1
3
2
3
6
7. . . 146
4
5
Sickle-cell hemoglobin
Figure 3.22
Protein Structure
• The shape (structure) of a
protein is intimately linked to its
function.
• Tertiary structure: how those
sheets or coils form a 3dimensional structure.
• In their role as enzymes, they
act as keys to make reactions
occur.
• Quaternary structure: using 2
or more tertiary structures to
create a more complex 3-D
structure.
• Primary structure: the linear
sequence of amino acids in a
chain.
• Secondary structure: the shape
the chain takes (sheet or coil).
• One more visual example…
Proteins have four levels of structure
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
http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf
Figure 3.23
http://www.stolaf.edu/people/giannini/flashanimat/proteins/hydrophobic%20force.swf
Facts about proteins
• Enzymes (proteins) are very
fragile: If you change just one
amino acid in the linear
sequence (primary structure),
you may impair the function of
the enzyme.
• Proteins are affected by pH and
temperature. If subjected to
high stress (extreme temperature
or pH), and protein may
denature (permanently change
its shape).
The structure of proteins
is very important!
• Diet: Proteins include eight essential amino acids
– Different
vegetables
contain
different ones;
BUT no single
vegetable
contains all
eight of them
– Meats, however,
do contain all eight
Essential amino
acids
Methionine
Valine
(Histidine)
Threonine
Corn and
other grains
Phenylalanine
Leucine
Isoleucine
Tryptophan
Lysine
Beans and
other
legumes
Summarizing Proteins
• Composed of 20 different
amino acids
• Amino acids joined by
peptide bonds
• Very complex 3dimensional structure
• Extremely important as
enzymes
• Energy density: 4
calories/gram
Nucleic Acids
• Not important in nutrition, but
famous because of DNA, RNA,
and ATP.
• Composed of nitrogenous base
(5 types), pentose sugar (2
types), and a phosphate group.
• They form chains of sugars
attached to phosphates (with the
nitrogenous base dangling.
•
DNA is double-stranded:
the nitrogenous bases in
adjacent strands attach to each
other.
•
Some nucleic acids are also
important in energetics. ATP
is the ‘currency’ used in the
cell to get things done.
Nucleic acids
• Nucleic acids are polymers
of nucleotides
• Nucleotides have three
parts:
– Sugar
– Phospate
– Nitrogen base
•
ATP (adenosine triphosphate)
Energetics and Respiration
How do living things work?
Order and Physical Laws
• Organisms require energy to
maintain order in their bodies.
• Without using energy to
maintain order, life would be
impossible.
• Why?
• Because of the 2nd Law of
Thermodynamics:
• Entropy (disorder) increases.
Order and Physical Laws
• 2nd Law of Thermodynamics:
• Entropy (disorder) increases.
• Restated in terms of chemical
reactions: No energy
transformation is 100%
efficient.
• What does that mean?
• It means energy is lost as heat
every time it changes forms.
• For example… when:
Sugar  ATP
glycogen  fat
fat  glycogen
Example of 2nd Law of Thermodynamics
• Consider a car that is powered
by gasoline.
• Most of the energy in the
gasoline is not used to propel
the car forward, play the stereo,
AC, etc.
• Rather it is wasted (lost) as heat.
• Much of the machinery under
your hood is designed to cool
the engine, not propel it!
Example #2
• Consider breakfast.
• If you eat a 500 calorie
breakfast, less than 200
calories are actually used
to produce ATP’s.
• The rest is lost as heat.
• Living cells and automobile engines use the same
basic process to make chemical energy do work
Fuel rich in
chemical
energy
Gasoline
Waste products
poor in chemical
energy
Heat
energy
Carbon dioxide
Combustion
Kinetic energy
of movement
Oxygen
Water
(a) Energy conversion in a car
Figure 5.3a
Fuel rich in
Chemical energy
Waste products poor
in chemical energy
Heat
energy
Gasoline
Carbon dioxide
Combustion
Kinetic energy
of movement
Oxygen
Water
(a) Energy conversion in a car
Heat
energy
Food
Oxygen
Cellular
respiration
Energy for cellular work
(b) Energy conversion in a cell
Carbon dioxide
Water
Types of energy
•
kinetic energy (moving objects)
1. moving car, moving baseball
2. hits something, stops, energy converted in sound,
heat, light, etc.
3. fire burning
•
potential energy (stored energy)
1. E.g. coiled spring, object at high location, gasoline
2. chemical energy is form of potential energy
Metabolism
• Living things maintain order through essential
chemical reactions called metabolism.
– Organic molecules are converted into other organic
molecules.
– Energy is released by oxidizing reduced carbon
compounds (that is, breaking lots of
C-H bonds).
Metabolism
Oxidation
• Both living creatures and fire consume oxygen.
The oxygen reacts with the fuel (wax in the candle,
or sugars in us) to produce CO2 and H2O. This
process is called oxidation. In our bodies we
oxidize glucose:
• C6H12O6 (glucose) + 6O2  6CO2 + 6H20
Differences between fire and metabolism
• Fire consumes everything: with enough oxygen, everything is oxidized
randomly and chaotically.
• But Metabolism is controlled and ordered. Energy is stored in ATP
molecules in your cells as the food molecules are oxidized slowly in
many small steps. And each small step requires an enzyme.
• How does your body control which molecules get oxidized, when, and
where?
• By producing the enzymes capable of certain reactions ONLY when those
reactions are needed.
What enzymes do
• Chemical reactions require a
push to get going.
• The push is called activation
energy.
• Enzymes reduce the activation
energy needed.
•http://www.lewport.wnyric.org/jwanamaker/animations/Enzyme%20activity.html
Facts about enzymes
• Lock and key idea: enzymes must have their own perfect
3-D shape.
Example: alcohol dehydrogenase
Facts about enzymes
• Enzymes are not used up in chemical reactions. They can
be reused over and over, and will continue to exist until
your body destroys them.
• Enzymes have very specific functions. Each step of a
chemical pathway requires a different enzyme.
Facts about enzymes
• Enzymes cannot get more
energy out of a reaction,
they just make reaction
more likely to occur.
Facts about enzymes
Enzyme activity
• Enzymes are temperature
sensitive, since proteins
denature at high
temperatures and lose their
shape.
Facts about enzymes
• Enzymes are sensitive to pH for the same reason.
Metabolism
• Living things require energy and materials to stay
alive.
– Energy and materials to maintain their structure and
function
– Energy and materials to reproduce
• Where does that energy come from?
Food webs and energy pyramids
Autotrophs and heterotrophs
• Autotrophs
– Make their own food/fuel
• Heterotrophs
– Need to consume food/fuel produced by autotrophs
• All organisms need to acquire materials from their
environment, but each type needs different
materials
Autotrophs
• Most make their own fuel by a
process called photosynthesis
• Have chlorophyll
• Convert CO2 and H2O to
C6H12O6 + O2
• Use solar energy to do this
Heterotrophs
• Must consume food for fuel
Respiration
• All eukaryotic cells burn fuel (glucose) to make ATP
• ATP can then be used as an energy source anywhere in the
cell or body.
• Burning fuel requires O2
• In cells the process is called respiration
Respiration
•
Respiration occurs in mitochondria
•
Respiration occurs in controlled steps each
step requires an enzyme
•
Glycolysis:
Glucose is split into 2 molecules – can occur
without O2, produces 2 ATP molecules
•
Krebs Cycle and Electron transport chain:
Require O2, produce 34 ATP molecules.
•C6H12O6 + O2 + ADP + P → CO2 + H2O + 36 ATP
Respiration Overview
Glucose
Glycolysis (sugar-breaking)
No O2
Fermentation
If O2 is present
Aerobic Respiration
Krebs Cycle
Electron Transport Chain
Respiration
• Other food we eat can also be burned for energy
Oxygen Cycle
• Respiration
C6H12O6 + O2→ CO2 + H2O
• Photosynthesis
CO2 + H2O → C6H12O6 + O2
• What’s wrong with this picture?
• Do plants use Oxygen? If so, what
for?
Energy vs. Materials
• Common elements in living things?
• Where do living things get these?
– Plants
– Animals
Energy vs. Materials
• It takes energy to stay alive
• What is the ultimate source of energy for all living
things?