Download Organic Molecule

In This Lesson:
Organic
Molecules in
Depth
(Lesson 8 of 9)
Today is Tuesday,
September 29th, 2015
• Pre-Class:
– Aldopentose is what kind of molecule?
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Carbohydrate
Lipid
Protein
Nucleic Acid
• Also, take a worksheet from the Turn-In box.
What’s in a name?
• Naming hints (write these on your key notes
page):
• If it ends in a(n):
– -ose, it’s probably a monosaccharide/disaccharide.
– -ine, it’s probably an amino acid or nucleotide.
– -ase, it’s probably an enzyme.
• These are not rules, but they are patterns.
Today’s Agenda
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Review
In-depth look at one organic molecule (carbs)
Review
In-depth look at one organic molecule (lipids)
Computer-based lab
By the end of this lesson…
• You should be able to identify detailed
characteristics of each of the four types
organic molecules and how they combine to
make life possible.
In-Depth Look Begins
• We now begin a closer look at each of the
organic molecules.
– Lots of info!
• First things first, though:
– The process of converting a monomer to a
polymer by linking monomers together is called
polymerization.
• (as in polymer-ization – makes sense)
In-Depth Look Begins
• Shapes of Organic Compounds
– Either ring-like or long chains:
http://faculty.clintoncc.suny.edu/faculty/Michael.Gregory/files/Bio%20100/Bio%20100%20Lectures/biochemistry/biochemi.htm
Carbohydrates
• Distinguishing Elements: C, H, O
• Used for short-term energy.
• Monomer: Simple sugars, also called
monosaccharides.
– Glucose - C6H12O6
– Fructose - C6H12O6
– Galactose - C6H12O6
• Chemical formulas are the same for each. It’s
all about what shape they take!
• Fun Fact: Glucose is also known as Dextrose.
Isomers
• Isomers are molecules with the same number
of atoms but different shapes.
– Glucose: 6 C, 12 H, 6 O
– Fructose: 6 C, 12 H, 6 O
– Difference? Shape. Glucose and fructose are
isomers.
Shapes of Monosaccharides
• Most of the time, scientists tend to draw
sugars in a ring shape.
http://faculty.clintoncc.suny.edu/faculty/Michael.Gregory/files/Bio%20100/Bio%20100%20Lectures/biochemistry/biochemi.htm
Monosaccharide Formula
• Simple sugars nearly always go by this
formula: CnH2nOn
• In other words, if n=6, the formula is:
– C6H12O6
• In fact, the above formula is almost always the
one for sugars.
– Sample test question coming next.
Sample Test Question
• Mrs. Anderson discovers a new molecule in her lab.
She doesn’t know what it is, but she remembers that
simple sugars often have the formula C6H12O6.
However, her molecule appears to be C2H4O2.
• What is the most specific hypothesis Mrs. Anderson
can draw about her molecule from her findings?
A.
B.
C.
D.
It’s probably a compound.
It’s probably an organic molecule.
It’s probably a carbohydrate.
No hypothesis can be drawn.
Carbohydrates
• Polymer: There are two general kinds of
polymers for carbohydrates.
– Disaccharides: Two monosaccharides linked.
– Polysaccharides: Three or more monosaccharides
linked.
Disaccharides
• Common Disaccharides:
– Sucrose: Glucose + Fructose
• Table sugar, beet sugar, cane sugar
– Lactose: Galactose + Glucose
• Milk sugar
– Maltose: Glucose + Glucose
• Malt sugar
Polysaccharides
• Chitin
– Insect exoskeletons and fungi
• Glycogen
– Used by animals to store energy (liver!)
• Starch
– Plant energy storage
• Cellulose
– Plant cell walls
Polysaccharides
Linking Monosaccharides
• Joined by glycosidic bonds (or C-O-C bridges):
Linking Monosaccharides
• Imagine a strange train.
-OH
Eiffel
Tower
Paper
Clips
>C=O
Snooki
• The contents of the train can be almost anything
as long as the links between them are the same.
– The links might as well be -OH and >C=O.
Linking Monosaccharides
• So it turns out that for two of the organic
molecules (carbs and proteins), there are
these things called functional groups on
either end of the monomer.
• These are parts of the monomer that are
always the same, even if the rest of the
monomer is different.
– Glucose, fructose, and galactose are obviously
different, but each have these two functional
groups.
C-O-C Bridges in Depth
• There are two functional groups are:
– Hydroxyl (sugar molecules have many)
• -OH
– Carbonyl (one per molecule)
• >C=O
• In linking, one molecule loses a hydroxyl group
and the other loses a hydrogen from a
hydroxyl group.
– Oxygen is left, the “-O-” in C-O-C bridge.
How Do Those Bridges Form?
• That part’s coming later on. For now, just roll
with it…
Building Carbohydrates
• With your lab group, build any two of the
following monosaccharides:
– Note the difference in shape, but not elements.
Carbon = Black 4-peg | Oxygen = Red 2-peg | Hydrogen = White 1-peg
End of Carbohydrates
• Take a look at your “Name That Carbon
Compound!” worksheets.
– Label all (and only) the carbohydrates you can find
on there before we move on to lipids.
Lipids
• Distinguishing Elements: C, H, O.
• Used for long-term energy storage among other
things.
• Remember that the closest thing to a monomer is
a triglyceride. There are 4 parts to a triglyceride.
– 1 glycerol molecule.
– 3 fatty acid chains. (this is where the tri in triglyceride
comes from)
– Picture next slide…
Triglyceride
Glycerol Molecule
http://www.indiana.edu/~oso/Fat/FatImg/triglyceride.jpg
Fatty Acid Chains
Saturated vs. Unsaturated
• This Example:
• Saturated Fat
– Straight Chain
• 9 Carbon Chain
• 19 Hydrogens
• Unsaturated Fat*
– Bent Chain
• 9 Carbon Chain
• 17 Hydrogens
– *Monounsaturated.
http://www.realfitnessblog.com/wp-content/uploads/2008/11/fat_f2.jpg
Blood Sugar
• Here’s something interesting involving lipids and
carbs in your bodies every day (it’s worth writing
down):
– Eating a meal increases blood sugar (carbohydrate).
– Exercise and stress also increase blood sugar.
– Glycogen is long-term carbohydrate storage (mostly in
the liver).
• In times of stress or exercise, glycogen is broken down into
glucose and released into the blood.
• Signaled by a hormone (lipid) called glucagon.
Blood Sugar
• When exercise or stress is over, or after a meal,
blood sugar needs to be removed or else you face
a condition known as hyperglycemia (generally
mild but irritating conditions).
• Your body uses a different hormone (a protein
hormone) called insulin to re-store glucose as
glycogen. Insulin is the only hormone that does
this.
• People that are diabetic tend to need boosts of
insulin to lower blood glucose levels.
Building Lipids
• With your lab group, build caproic acid.
Carbon = Black 4-peg | Oxygen = Red 2-peg | Hydrogen = White 1-peg
End of Lipids
• Take a look at your “Name That Carbon
Compound!” worksheets.
– Label all (and only) the lipids you can find on there
before we move on to proteins.
Proteins
• Proteins are important for a lot of things in the
body. Among others, proteins include:
– Enzymes (to speed up reactions)
– Antibodies (to fight off infections)
– Keratin or collagen (to form skin, hair, nails,
feathers, scales)
– Some hormones (including insulin, notably)
Proteins
• Distinguishing Elements: C, H, O and N
• Amino acids also have functional groups on
either end of the molecule:
– One end has an amino group (NH2).
– Other end has a carboxyl group (COOH).
• Amino acids are a very diverse group:
– Some polar, some non-polar, some have rings,
some enjoy long walks on the beach and
scrambled eggs.
• Last one just to make sure you’re not asleep…
Functional Groups
• Functional groups:
– Amino (-NH2)
– Carboxyl (-COOH)
– Rest of amino acid (“R”)
• (technically “radical”)
• Protein Bonds:
– Amino acids bond with
one another through
peptide bonds.
http://upload.wikimedia.org/wikipedia/commons/0/0f/Alpha-amino-acid-2D-flat.png
Functional Groups
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/aminoab.gif
Building Proteins
• Before we build a whole amino acid, first build
the generalized structure:
– Leave out the “R” group for now.
Carbon = Black 4-peg | Oxygen = Red 2-peg | Hydrogen = White 1-peg
Nitrogen = Blue…uh…2-peg?
Amino Acids
• Keep this listing of amino acids safely in your
notebooks. We’re returning to this much later
in the year.
• For now, let’s have some fun with
pronunciation.
– First, all of the ones ending in “ine” sound like
“eene.”
Amino Acid Pronunciation
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Alanine
[al-uh-neen]
Arginine
[ar-ji-neen]
Aspartic Acid
[a-spar-tick acid]
Glutamic Acid
[glue-tamic acid]
Glutamine
[glue-ta-meen]
Glycine
[glei-seen]
Proline
[pro-leen]
Serine
[serene]
Asparagine
[as-par-uh-gene]
Cysteine
[sis-teen]
Tyrosine
[ty-row-seen]
The above are non-essential amino acids.
– Can be made by the human body.
Amino Acid Pronunciation
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Isoleucine
[ey-so-loo-seen]
Leucine
[loo-seen]
Lysine
[ly-seen]
Methionine
[meth-eye-oh-neen]
Phenylalanine
[fen-ill-al-uh-neen]
Tryptophan
[trip-toe-fan]
Threonine
[three-oh-neen]
Valine
[vay-leen]
Histidine
[his-ti-deen]
The above are essential amino acids.
– They cannot be made by the human body.
Proteins
• Don’t forget that enzymes are very important
protein molecules.
• Enzymes catalyze (help start) chemical
reactions.
– Without enzymes, life as we know it would not be
possible.
One last note on Proteins…
• Contrary to popular marketing, proteins do not
provide energy directly to the body.
• This is why marathon runners don’t eat
hamburgers the night before a race.
• Analogy:
– Solar power plants use the sun to create electricity.
The sun is the energy source.
– There are people working there too, but they don’t
make electricity. They just help the sun get converted
into electricity.
– In living things, lipids and carbohydrates provide the
energy. Proteins just help use it.
Building Proteins
• With your lab group, complete the amino acid
model you previously assembled, filling in the
R group accordingly.
Carbon = Black 4-peg | Oxygen = Red 2-peg | Hydrogen = White 1-peg
Nitrogen = Blue…uh…2-peg?
Aside: Protein Structure
• Proteins have four levels of structure.
– Primary: the string of amino acids.
– Secondary: when the string of amino acids bends
into different shapes in different regions.
– Tertiary: when the different shapes join together.
– Quaternary: multiple proteins put together in
tertiary structure.
• Example next slide…
Aside: Protein Structure
Chain of Amino Acids ------>
Shapes that regions of the
amino acid chain make ---->
Interactions between the
shapes ---->
Multiple tertiary-structure
protein units ---->
http://upload.wikimedia.org/wikipedia/commons/a/a6/Protein-structure.png
Aside: Protein Structure
http://www-3.unipv.it/webbio/anatcomp/freitas/2008-2009/protein_structure.jpg
Aside: Protein Structure
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Spombe_Pop2p_protein_structure_rainbow.png
http://depts.washington.edu/phcol/images/6_protein_structure.jpg
/350px-Spombe_Pop2p_protein_structure_rainbow.png
Protein Structure Video/Game
• FoldIt
End of Proteins
• Take a look at your “Name That Carbon
Compound!” worksheets.
– Label all (and only) the proteins you can find on
there before we move on to nucleic acids.
Before we get to Nucleic Acids…
• Let’s take a little break and do an e-Lab.
• It’s called Identifying Nutrients and it’s on
ExploreLearning.
• There’s a Quia quiz called “Identifying
Nutrients Gizmo” that you’ll need in a new
window to guide your work.
• [Log-in Instructions]
Nucleic Acids
• Distinguishing Elements: C, H, O, N, and P
• Remember that DNA and RNA are examples of
nucleic acids.
– DNA – Deoxyribonucleic Acid
– RNA – Ribonucleic Acid
[dee-oxy-ry-bo]
[ry-bo]
• The monomer of a nucleic acid is a nucleotide.
• A nucleotide is made of three separate parts.
– Next slide…
Nucleic Acids
• Each nucleotide has a:
– Sugar molecule with 5-carbons (pentose)
• Deoxyribose in DNA
• Ribose in RNA
– Phosphate group
• Phosphorus-based molecule
– Nitrogenous base (makes the nucleotide unique)
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Adenine
Thymine
Cytosine
Guanine
Nucleotide Structure
Guanine
Adenine
Thymine
Cytosine
http://www.biologyjunction.com/images/nucleotide1.jpg
Nucleotide Structure
• More “scientific”
Ribozymes
• This won’t be on your test, but
it’s interesting either way.
• In looking for ways life may have
gotten started on earth,
biochemists identified things
called ribozymes. These are bits
of RNA (nucleic acid) that act
like enzymes (protein).
– Since it’s both genetic material
and capable of catalyzing
reactions, it may be the
precursor to other organic
molecules and/or life!
http://ndbserver.rutgers.edu/atlas/xray/indexes/xray.ribozyme-1.gif
One last thing…
• One nucleotide is linked to another nucleotide
with a phosphodiester bond, sometimes
called a 3’-5’ phosphodiester bond.
– Pronounced “3 prime, 5 prime fahs-fo-die-ester
bond.”
– More on this later (like three units later)…
– For the test, please do know what a
phosphodiester bond links.
End of Nucleic Acids
• Take a look at your “Name That Carbon
Compound!” worksheets.
– Finish it!
Exclusion Brainstorming
• Another round of “which one of these things
is not like the other…”
• Talk to your partners!
• Use the whiteboards and your notebooks.
– Avoid doodling.
Exclusion Brainstorming
• Example 1:
– Sucrose, fructose, glucose, galactose
• Answer: Sucrose – not a monosaccharide.
• Example 2:
– Isoleucine, glycine, adenine, glutamine
• Answer: Adenine – not an amino acid.
• Example 3:
– Adenine, thymine, cytosine, cysteine
• Answer: Cysteine – not a nucleotide (nitrogenous base).
• Example 4:
– Starch, glycogen, chitin, cellulose
• Answer: Glycogen – only one humans make.
Exclusion Brainstorming
• Example 5:
– Fatty acid, steroid, triglyceride, glycerol
• Answer: Steroid – only one not part of a triglyceride.
• Example 6:
– Bent fatty acid, unsaturated, liquid, solid
• Answer: Solid – all others concern unsaturated fats (oils).
• Example 7:
– C-O-C bridge, disaccharide, maltose, glucose
• Answer: Glucose – all others are related to carbohydrate polymers.
• Example 8:
– Peptide bond, phosphate group, nitrogenous base, 5carbon sugar
• Answer: Peptide bond – all others are related to nucleotide
structure.
Organic Molecule Market
• Version 2.0
Quia Review (In Order)
• Organic Molecule Fill-In
• Organic Molecule Matching
• Organic Molecule Challenge Board
– Put away one computer and get a partner for this
one.
Closure Chart
Organic
Molecule
Carbohydrate
Lipid
Protein
Nucleic Acid
Monomer
Polymer(s)
Bonds
Elements
Closure Chart
Organic
Molecule
Monomer
Polymer(s)
Bonds
Elements
Carbohydrate
Monosaccharide
Disaccharides,
Polysaccharides
Glycosidic Bonds
C, H, O
Lipid
Triglyceride
(sort of)
N/A
N/A
C, H, O
Protein
Amino Acid
Polypeptide
Peptide Bonds
C, H, O, N
Nucleic Acid
Nucleotide
Nucleic Acid
Phosphodiester
Bonds
C, H, O, N, P