Transcript Unit 3 Macromolecules, Enzymes, and ATP

Unit 3
Macromolecules, Enzymes, and ATP
Mrs. Stahl
AP Biology
Organic chemistry is the study of
carbon compounds
• Organic chemistry is the study of compounds
that contain carbon
• Organic compounds range from simple
molecules such as methane- CH4 to colossal
ones like proteins.
• Most organic compounds contain hydrogen
atoms in addition to carbon atoms
• Percentages of the major elements are pretty
consistent from one organism to another,
however they can be utilized in many different
ways.
• Different species of organisms and individuals
within the same species are distinguished by
their differences in organic molecules (DNA,
enzymes, etc).
How did it all begin?
• Scientists wanted to learn how to purify and
improve substances such as food, medicine and
fabrics, which are all obtained from living things.
• 1800’s- Chemists were making things in the lab by
combining elements under the right conditions.
• They believed that artificial synthesis (recreating
molecules) in the lab was impossible.
• Vitalism was the belief that organic compounds
could only arise in living organisms.
• Vitalism was disproved when chemists were able to
synthesize organic compounds
Example
• 1928- urea was accidentally created in a lab by a
German chemist, Friedrich Wohler
• He was trying to make an inorganic salt called
ammonium cyanate by mixing ammonium and cyanate
ions but made urea instead. Urea is an organic
compound that is found in the urine of mammals.
• Scientists (Vitalists) were not convinced because the
cyanate was extracted from animal blood.
• Vitalism crumbled after several decades of synthesizing
complex organic compounds. Thoughts shifted from
vitalism to mechanism.
• Mechanism- physical and chemical laws govern all
natural phenomena. Redefined organic chemistry as
the study of carbon compounds, regardless of origin.
Stanley Miller’s Synthesis
• His synthesis of organic compounds related to
evolution
• Miller tested whether complex organic molecules
could arise spontaneously under conditions thought
to have existed on early Earth (abiotic factors).
Experiments support the idea that abiotic synthesis
of organic compounds, perhaps near volcanoes,
could have been a stage in the origin of life
• 1953- set up a closed system to simulate conditions
thought to have existed on early Earth.
The Experiment
• 1. Water mixture in “sea” flask was heated; vapor
entered atmosphere flask.
• 2. “Atmosphere” flask contained a mix of hydrogen gas,
methane, ammonia, and water vapor
• 3. Sparks were discharged to mimic lightning
• 4. Condenser cooled the “atmosphere,” “raining” water
and any dissolved molecules down into the sea flask
• 5. Material cycled through the apparatus and Miller
periodically collected samples and analyzed them
“Atmosphere”
CH4
Water vapor
Electrode
Condenser
Cooled “rain”
containing
organic
molecules
H2O
“sea
”
Sample for
chemical analysis
Cold
water
Results
• Miller was able to identify a variety of organic
molecules such as formaldehyde, hydrogen
cyanide, and complex amino acids and
hydrocarbons.
• Organic molecules may have been synthesized
abiotically on early Earth.
Carbon: The Backbone of Life
• Living organisms consist mostly of carbon-based
compounds
• Carbon is unparalleled in its ability to form large,
complex, and varied molecules
• Proteins, DNA, carbohydrates, and other molecules
that distinguish living matter are all composed of
carbon atoms bonded to one another and to other
elements (H, O, N, S, and P).
• Carbon enters the planet through plantsphotosynthesis. Plants take CO2 from the atmosphere
and transforms it into usable forms of energy –
glucose (C6H12 O6) and O2, which are passed along to
animals through the process of cellular respiration.
CARBON!!!
Carbon can
form up to
four covalent
bonds!
Carbon can bond to four other atoms or
groups of atoms, making a large variety of
molecules possible.
• The electron configuration of carbon gives it
covalent compatibility with many different
elements
• The valences of carbon and its most frequent
partners (hydrogen, oxygen, and nitrogen) are
the building code for the architecture of living
molecules
• Carbon atoms can partner with atoms
other than hydrogen; for example:
– Carbon dioxide: CO2
– Urea: CO(NH2)2
Molecular Diversity Arising from
Variation in Carbon Skeletons
• Carbon chains form the skeletons of most
organic molecules
• Carbon chains vary in length and shape
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
Animation: Carbon Skeletons
Hydrocarbons
• Hydrocarbons are organic molecules consisting of only
carbon and hydrogen. Very common on Earth.
• Attached to carbon skeleton wherever electrons are
available for covalent bonding
• Many organic molecules, such as fats, have
hydrocarbon components that serve as stored fuel for
animals
• Hydrocarbons can undergo reactions that release a
large amount of energy
• Major components of petroleum. Petroleum is called a
fossil fuel because it is partially made up of
decomposed remains that lived millions of years ago.
Hydrocarbon Fun Facts
• NONPOLAR- do they dissolve in water?
• Hydrophobic
• Have the potential to release a lot of energy
through reactions
• The gas in your car is made up of them
Nucleus
Fat droplets
10 μm
(a) Part of a human adipose cell
(b) A fat molecule
Functional Groups
• Carbon and Hydrogen have similar electronegativities
with evenly distributed electrons that is why they are
nonpolar.
• There are other biological molecules in cells that
contain other atoms with different electronegativities
that are partially positive and negative, making them
polar.
• These groups can be referred to as the C-H core group
where other molecules known as functional groups can
attach to.
• -OH is a common functional group, aka hydroxyl group
• The seven functional groups that are most
important in the chemistry of life
– Hydroxyl group
– Carbonyl group
– Carboxyl group
– Amino group
– Sulfhydryl group
– Phosphate group
– Methyl group
Chemical Group
Hydroxyl group (—OH)
Compound Name
Examples
Alcohol
Ethanol
Carbonyl group (
C＝O)
Ketone
Aldehyde
Acetone
Carboxyl group (—COOH)
Propanal
Carboxylic acid, or
organic acid
Acetic acid
Amino group (—NH2)
Amine
Glycine
Sulfhydryl group (—SH)
Thiol
Cysteine
Phosphate group (—OPO32−)
Organic
phosphate
Glycerol phosphate
Methyl group (—CH3)
Methylated
compound
5-Methyl cytosine
Isomers
• Isomers are compounds with the same molecular
formula but different structures and properties
– Structural isomers have different covalent arrangements
of their atoms (carbon skeleton). Example-glucose
– Stereoisomers (Cis-trans isomers / Geometric Isomers)- have the same carbon skeleton but differ in how the
groups are attached / three dimensional shape in space.
• Enantiomers are isomers that are mirror images
of each other
Enantiomers
• Chiral molecule- molecule that has mirror
image versions and typically occurs when
carbon is bound to four different molecules.
• Think of them as left handed and right
handed. Just as your right hand won’t fit into a
left handed glove, the molecules working in
the cell can tell the difference between the
two versions by shape. One is typically active,
while the other is inactive.
– Enantiomers are really important in the pharmaceutical
industry because two enantiomers of a drug may not be
equally effective and can sometimes have harmful effects.
– Example: Thalidomide was a drug prescribed for 1000s of
pregnant women in the late 50's, early 60's. This drug was
a mixture of two enantiomers: one that would reduce
morning sickness, and the other caused severe birth
defects such as shortened arms and legs, blindness,
deafness, heart problems, and brain damage
(http://www.bbc.com/news/uk-england-23500853).
– The differing effects of enantiomers in the body
demonstrate that organisms are sensitive to even the
most subtle variations in molecular structure and design.
(a) Structural isomers
Pentane
2-methyl butane
(b) Cis-trans isomers
cis isomer: The two Xs are
on the same side.
trans isomer: The two Xs are
on opposite sides.
(c) Enantiomers
CO2H
CO2H
C
H
C
NH2
CH3
L isomer
NH2
H
CH3
D isomer
Animation: Isomers
Figure 4.7a
(a) Structural isomers
Pentane
2-methyl butane
Figure 4.7b
(b) Cis-trans isomers
cis isomer: The two Xs are
on the same side.
trans isomer: The two Xs are
on opposite sides.
Figure 4.7c
(c) Enantiomers
CO2H
CO2H
C
H
C
NH2
CH3
L isomer
NH2
H
CH3
D isomer
The Molecules of Life
• All living things are made up of four classes
of large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
• Macromolecules are large molecules and are
complex
• Large biological molecules have unique
properties that arise from the orderly
arrangement of their atoms
Figure 5.1
Macromolecules are polymers, built
from monomers
• A polymer is a long molecule consisting of many
similar building blocks
• The repeating units that serve as building blocks
are called monomers
• Three of the four classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
The Synthesis and Breakdown of
Polymers
• Enzymes are specialized macromolecules that
speed up chemical reactions such as those
that make or break down polymers
• A dehydration reaction occurs when two
monomers bond together through the loss of
a water molecule
• Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction
Understanding Dehydration Synthesis
and Hydrolysis
• See the board and copy into your notes 
Where do we get proteins from?
• Amino Acids
• Ex- We eat a steak-> goes into our digestive
system where hydrolysis occurs and the
protein is broken down into amino acids->
weave it back together to form a polymer so
that it can make a protein and functions can
be carried out.