in this lesson: today is tuesday, september 29th, 2015 · •review •in-depth look at ......

Today is Tuesday,September 29th, 2015

• Pre-Class:

– Aldopentose is what kind of molecule?

• Carbohydrate

• Lipid

• Protein

• Nucleic Acid

• Also, take a worksheet from the Turn-In box.

In This Lesson:Organic

Molecules in Depth

(Lesson 8 of 9)

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

• 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. It’s probably a compound.

B. It’s probably an organic molecule.

C. It’s probably a carbohydrate.

D. 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):


• Imagine a strange train.

• 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.

Eiffel Tower

SnookiPaper Clips

-OH >C=O


• 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

http://www.indiana.edu/~oso/Fat/FatImg/triglyceride.jpg

Glycerol Molecule Fatty Acid Chains

Saturated vs. Unsaturated

http://www.realfitnessblog.com/wp-content/uploads/2008/11/fat_f2.jpg

• This Example:

• Saturated Fat

– Straight Chain

• 9 Carbon Chain

• 19 Hydrogens

• Unsaturated Fat*

– Bent Chain

• 9 Carbon Chain

• 17 Hydrogens– *Monounsaturated.

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


– 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-pegNitrogen = 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

• 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

• 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-pegNitrogen = 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…


http://upload.wikimedia.org/wikipedia/commons/a/a6/Protein-structure.png

Chain of Amino Acids ------>

Shapes that regions of the amino acid chain make ---->

Interactions between the shapes ---->

Multiple tertiary-structure protein units ---->


http://www-3.unipv.it/webbio/anatcomp/freitas/2008-2009/protein_structure.jpg


http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Spombe_Pop2p_protein_structure_rainbow.png/350px-Spombe_Pop2p_protein_structure_rainbow.png

http://depts.washington.edu/phcol/images/6_protein_structure.jpg

Protein Structure Video/Game

• FoldIt

End of Proteins


– 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 [dee-oxy-ry-bo]

– RNA – Ribonucleic Acid [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)• Adenine

• Thymine

• Cytosine

• Guanine

Nucleotide Structure

http://www.biologyjunction.com/images/nucleotide1.jpg

AdenineThymineCytosineGuanine

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


– 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.


• 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.


• 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, 5-

carbon 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

Monomer Polymer(s) Bonds Elements

Carbohydrate

Lipid

Protein

Nucleic Acid

Closure Chart

Organic Molecule

Monomer Polymer(s) Bonds Elements

Carbohydrate MonosaccharideDisaccharides,

PolysaccharidesGlycosidic Bonds C, H, O

LipidTriglyceride

(sort of)N/A N/A C, H, O

Protein Amino Acid Polypeptide Peptide Bonds C, H, O, N

Nucleic Acid Nucleotide Nucleic AcidPhosphodiester

BondsC, H, O, N, P

in this lesson: today is tuesday, september 29th, 2015 · •review •in-depth look at ......

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