Today is Wednesday,October 15th, 2014

Pre-Class:You remember the four types of organic

molecules, don’t you? DON’T YOU?

Please turn in your Root Words for Unit 3.

In This Lesson:Biochemistry

(Lesson 2 of 5)

Today’s Agenda

• Basic chemistry and biochemistry.• Basic organic chemistry.• Basically, a review of a lot of stuff you’ve

learned already.– Plus some stuff you didn’t.

• Where is this in my book?– Chapter 5 and a little bit of 4.

By the end of this lesson…

• You should be able to describe the four basic molecules that make up just about everything organic.

• You should be able to explain why carbon is the primary element of life.

• You should be able to categorize molecules in terms of chemical properties based on functional groups.

Where to begin…?

• I could begin with a review of atomic structure (protons, neutrons, electrons), but you already know that.

• And you already know that the number of protons is equal to the atomic number.

• And you know that the mass number of an atom is the number of protons plus the number of neutrons, so I can skip that.

• You’re good with the whole, “valence electrons are the outermost electrons” thing too.

• What else can I skip?

Where to begin…?

• I guess I don’t need to tell you that ionic bonds involve a transfer of electrons, while covalent or molecular bonds involve a sharing or fighting-over of electrons.

• You’re also completely solid on the idea that the electrons, being located at a distance from the nucleus, are the only things involved in bonding directly.

• So that’s good. I guess we can skip straight to the new material.– I guess we should probably review first, though.

Video Review

• CrashCourse – That’s Why Carbon is a Tramp

Carbon

• Carbon is uniquely positioned on the periodic table as it has only four valence electrons, allowing it to form one, two, three, or four bonds.– Other elements also have four valence electrons, but

they’re not as small nor as plentiful as carbon.• Thanks to the fact that carbon can form so many

different bonds, and thus form many larger building blocks, any compound containing carbon and hydrogen is called an organic compound.– In fact, organic chemistry is an entire (challenging) branch

of chemistry devoted to the study of carbon compounds.

Sample Carbon Compounds

Organic Chemistry Vocabulary

• Before we get into the big molecules formed by carbon, let’s look at the little “attachments” that you’ll find on the main molecule.

• Keep in mind, most hydrocarbons are non-polar and therefore hydrophobic.

• These molecular attachments, called functional groups, change the characteristics of the molecule.– Like branches from a tree.– Like pimples on a teenage hydrocarbon’s face.

Let’s start slow…Hydroxyl Group

• Hydroxyl = -OH– Note: Hydroxide = OH- - that’s different.

• Important Properties– It’s polar/hydrophilic, so molecules containing it

can usually dissolve.– A molecule containing this group is known as an

alcohol (“____ol”).

Carboxyl Group

• Carboxyl = -COOH• Important Properties– Polar/hydrophilic.– Acts as an acid by donating its hydrogen atom (H+).– Common in carbon-based acids.– A molecule containing this group is known as a

carboxylic acid or organic acid.

Amino Group

• Amino = -NH2

• Important Properties– Polar/hydrophilic.– Acts as a base by receiving H+ ions.

• This is the Brønsted-Lowry base definition.

– A molecule containing this group is known as an amine.• Note: Amino acids commonly have both amines and

carboxylic acids on their molecules.• Whether the entire molecule acts as a base or an acid

depends on the pH of the surrounding solution.

http://chemistry2.csudh.edu/rpendarvis/aminoacids.html

Sulfhydryl Group

• Sulfhydryl = -SH• Important Properties– Very weakly polar.– Found in proteins to help tertiary and quaternary structure.– Think of them as “shapers.”

• Book example: This is what makes hair stay curly or straight and sulfhydryl-containing compounds are used in perms to change the natural structure.

– A molecule containing this group is known as a thiol.– Fun fact: Thiols are used as the smell in natural gas.

Phosphate Group

• Phosphate = -OPO32-

• Important Properties– Provides a 1- or 2- charge.– Can react with water to release energy.• Look for this group in ATP and other nucleotides (like DNA).

– A molecule containing this group is known as an organic phosphate.

Methyl Group

• Methyl = -CH3

• Important Properties– Non-polar and unreactive…that’s the point of a

methyl group.– Often methyl groups are used to deactivate portions

of DNA and larger molecules.– A molecule containing this group is known as a

methylated compound.

Back to Carbon

• Because carbon can form MASSIVE structures, it’s best to break them down into their basic building blocks.

• Hence:– Monomers are the basic building blocks.

• Mono – get it?

– Polymers are the large complex chains of monomers.• Poly – want a cracker?

– Macromolecules are the big four categories of polymers out there.

The Four Macromolecules

• The four organic molecules are:– Carbohydrates– Lipids– Proteins– Nucleic Acids

• They each have some defining features:– Composition– Functional Groups

But, before we get to them…

• It’s at this point that I hope a certain thought has crossed your mind.

• We’re talking about atoms and now are talking about the molecules they form in combination with one another.

• Exactly where does “life” come into play?• Living things are composed of non-living atoms.– Read that again. We’re going to take a couple

minutes to just…think about that.

(Also) About Functional Groups

• 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 called functional groups.– As we’ve seen, they impart certain properties to

molecules and also help to link them.

Paper Clips BiebsThe Lost

Ark

-OH >C=O

Functional Groups

• Again, functional groups are small clusters of atoms present in larger monomers.– They’re not part of the hydrocarbon – the long

chain of…hydrogens and carbons.• They give the molecule its properties,

especially in linking it to other molecules.

How small are we talking?

• Scale of the Universe!– Scale of the Universe

Heads-Up

• On the next slides, we’re going to examine each of the organic molecules one-by-one.– First Slide: Summary– Then: Monomer Detail– Then: Polymer Detail(s) and Examples– Then: Summary again

• However, we’re going to explore some additional details in the carbohydrate section regarding bonding and “unbonding,” so leave about a quarter of the page blank right now.– We’ll fill it in later.

!

#1 – CarbohydratesSummary

• Composition: C, H, O• Functional Group(s): -OH [hydroxyl group]• Function(s): Energy source, plant building

material, cell markers.• Monomer: Monosaccharide• Polymer: Disaccharide, polysaccharide

#1 – CarbohydratesMonomers

• Carbohydrate monomers can be spotted by the 1:2:1 pattern of their C, H, O atoms.

• Example: Glucose (cell fuel) is C6H12O6

• Example: Fructose (very sweet) is C6H12O6

• Example: Galactose (milk sugar) is C6H12O6

• The difference? Their shapes.– Because they’re all the same formula, they’re called

isomers of one another.• Iso- (same)

Aside: Sugar is Sweet (!)

• There are lots of sugars out there and they can be ranked by “sweetness.” Here are a few, all compared to sucrose (table sugar).– Lactose: Not as sweet.– Maltose: Equal sweetness.– Glucose: Slightly sweeter.– Fructose: 4x sweeter.– Aspartame*: 150x sweeter.– Saccharine*: 450x sweeter.– Sucralose*: 600x sweeter.– Neotame*: 8000x sweeter. *Artificial sweeteners

#1 – CarbohydratesFunctional Groups

• Remember, -OH (hydroxyl) is the functional group for carbohydrates.

#1 – CarbohydratesDisaccharides

• A disaccharide, like the name suggests, is simply two linked monosaccharides.– The monosaccharides were linked by a

dehydration synthesis reaction – details next slide.• Examples:– Glucose + Glucose = Maltose (malt sugar)– Glucose + Fructose = Sucrose (table sugar)– Glucose + Galactose = Lactose (milk sugar)

Dehydration Synthesis

• Do I really need to tell you what happens in a dehydration synthesis reaction?– Follow the word stems!

• Water…• …is removed…• …to put things

together.• Sure enough…

Hydrolysis

• The opposite of dehydration synthesis is hydrolysis.– Follow the word stems!

• Water…• …breaks apart.• Think of it like “hydro-

slices.”• Sure enough…

Isomers

• Did you happen to notice something about the formulas of glucose and fructose on the previous slide?

• Take another look:

• Molecules with the same formula but different shapes are called isomers.

#1 – CarbohydratesBonds

• Once the bond has formed, it’s known as a glycosidic bond, less commonly as a C-O-C bridge.

#1 – CarbohydratesPolysaccharides

• A polysaccharide is a complex molecule made of three or more monosaccharides.– Example: Starch (plant sugar storage)– Example: Glycogen (animal sugar storage –

muscles)– Example: Cellulose (cell walls – fiber)– Example: Chitin (insect exoskeletons – crunch)

#1 – CarbohydratesExamples

#1 – CarbohydratesSummary

• Composition: C, H, O• Functional Group(s): -OH [hydroxyl group]• Function(s): Energy source, plant building

material, cell markers.• Monomer: Monosaccharide– Glucose, fructose, galactose.

• Polymer: Disaccharide, polysaccharide– Disaccharide: Sucrose, maltose, lactose– Polysaccharide: Starch, glycogen, cellulose

#2 – LipidsSummary

• Composition: C, H, O (except they’re mostly non-polar).

• Functional Group(s): Carboxyl [-COOH]...sorta.• Function(s): Fats, oils, waxes, steroids, cholesterol,

hormones, pigments…and energy storage.• Monomer: Um…• Polymer: Sigh…

• Lipids are weird. The best thing you can do is remember that.

#2 – LipidsMonomers

• There is no true monomer for lipids.• That said, many lipids contain something

called a triglyceride, which is made of a glycerol molecules along with three (tri) fatty acids.

Glycerol Molecule Fatty Acid Chains

Fatty Acids• What do you see here on this fatty acid?– First, there’s a long hydrocarbon chain.– Highlighted in red(ish) is the functional group –

carboxyl – given by –COOH.– The carboxyl is the only polar part.

Fatty Acids

• Fatty acids also govern the nature of the lipid:• Are all hydrocarbon bonds single?– The fat is saturated (with H) and is a solid at room

temperature.• Fatty acid tails can pack tightly together to form a solid.• Each carbon in the chain is bound to four atoms.

Fatty Acids

• Are some bonds double?– The fat is unsaturated (with H) and is liquid at

room temperature – an oil.• Kinked fatty acid tails can’t pack closely together,

keeping the substance a liquid.• Some carbons have double bonds and therefore are

bonded to only three other atoms.

Aside: Hydrogenation• You may have seen the term

“partially hydrogenated” or “fully hydrogenated” in a food product (peanut butter’s a big one).– Maybe you’ve heard of trans fats?

• Hydrogenation in food products is the forced addition of hydrogen to unsaturated fats in order to make them saturated.

• Trans fats can be formed when the hydrogenation process doesn’t fully saturate the oil.– They’s bad for you. Avoid ‘em.

http://media.fooducate.com/blog/posts/regularjif.jpg

Lipid TypesType Triglyceride Phospholipid Steroid

Structure3 nonpolar fatty

acids, 1 polar glycerol molecule

2 nonpolar fatty acids, 1 phosphate group, 1 glycerol molecule (polar)

4 fused rings plus functional group

Function Storage of energy Cell membrane composition

Cell membranes (cholesterol),starting material for sex

hormones

Lipid Stuff

• With no true monomer, lipids have no real polymers either, and they don’t have characteristic bonds.

• Keep in mind one extra thing, though:– Carbohydrates and lipids both provide the cell

with energy, but lipids tend to be a longer-term source of energy.

#2 – LipidsSummary

• Composition: C, H, O (except they’re mostly non-polar).

• Functional Group(s): Carboxyl [-COOH]...sorta.• Function(s): Fats, oils, waxes, steroids, cholesterol,

hormones, pigments…and energy storage.• Monomer: Um…• Polymer: Sigh…

• Lipids are weird. The best thing you can do is remember that.

#3 – ProteinsSummary

• Composition: C, H, O, N• Functional Group(s): Amino group [-NH2],

carboxyl group [-COOH]• Function(s): Enzymes, receptors, structural

components, skin, hemoglobin, antibodies…the list goes on.

• Monomer: Amino acid• Polymer: Polypeptide

#3 – ProteinsMonomer and Functional Groups

• Each amino acid has a central carbon…• …an amino group (NH2) and carboxyl group (COOH)…• …a hydrogen…• …and the R (radical) group which is different for each amino

acid)…

#3 – ProteinsStructure

• Key: Amino acids take an N-C-C central structure.• Key: The central C has an H on one side and the R-

group comes off the other.

#3 – ProteinsMonomers

• There are 20 very different amino acids.

• Key: The R-group gives the amino acid its traits.

• Consider them the “alphabet of life.”– Look at the

headings for the various groups:

http://nobelprize.org/educational/medicine/dna/a/translation/aminoacids.html

#3 – ProteinsPolymers and Bonds

• Dehydration synthesis reactions allow for the joining of amino acids into dipeptides and polypeptides.– The bonds between them are called peptide

bonds.– Peptide bonds link a nitrogen and carbon (N-C).

• Let’s take a look…

#3 – ProteinsBonds

Protein Structure

• Okay, this gets a little complicated.• Completed polypeptides have four levels of

structure.• We’re going to look at the steps on new slides.• Before that, one more bond type:– A disulfide bond occurs in proteins and joins two

sulfhydryl (-HS) groups.

Primary Protein Structure

• First, the amino acids must be linked together in a particular order by peptide bonds.– Example: Methionine, cysteine, proline, proline.

Secondary Protein Structure

• Because of the different properties of amino acids, segments of the protein fold into particular shapes called either an alpha (α) helix or a beta (β) pleated sheet.– These are caused by hydrogen bonds linking functional groups.

Secondary Protein Structure

• Alpha Helix and Beta Pleated Sheet

http://www.mun.ca/biology/scarr/MGA2-03-25.jpg

Tertiary Protein Structure

• The α helices and β sheets then fold onto each other and the R-groups interact.– Hydrophobic interactions, ionic bonds, disulfide bonds, and hydrogen

bonds play roles here.• This produces a structure called a globular subunit (basically just a

protein in tertiary structure).

Quaternary Protein Structure

• Quaternary structure is just a combination of two or more globular subunits (tertiary structure proteins).– Hydrophobic interactions, ionic bonds, disulfide bonds, and

hydrogen bonds play roles here.• Hemoglobin, for example, has four subunits.

Protein Folding Summary

• Primary: The string/order of amino acids.– Peptide bonds.

• Secondary: Formation of α-helices and β-sheets.– Hydrogen bonds (between functional groups).

• Tertiary: Folding of α-helices and β-pleated sheets onto themselves.– R-group interactions: ionic bonds, hydrophobic

interactions, and hydrogen bonds.• Quaternary: Tertiary subunits put together, using

the same type of bonds/interactions.

Aside: FoldIt

• The best kind of game…

Protein Structure Activity

• Everyone grab a cup (don’t break it) and fill it about halfway with water – you’re going to be an amino acid.

• As you know, reactions that put monomers together are dehydration synthesis reactions, so since you’re each free monomers, you still have your H2O.

• We’re going to head into the halls and do a classroom bonding activity (in several ways).

Protein Structure Activity• Why did we dump water out?

– To simulate dehydration synthesis.• What type of bond was represented by hand-holding?

– Peptide bonds.• Before I told you how to fold (the first time), what level of protein

structure were we modeling?– Primary structure.

• After we folded the first time, what structure was formed?– Secondary structure.

• What bonds formed to allow us to fold into secondary?– Hydrogen bonds.

• When I told you who was hydrophobic, what types of bonds were formed?– R-group interactions (H-bonds, hydrophobic interactions, ionic bonds).

• Why did we need to hide hydrophobic (nonpolar) amino acids?– Because most of the surroundings are water.

Denaturation

• Expose a protein to high heat or different pH levels and you can denature it (essentially deforming/breaking it).– Think about how the liquid part of eggs become

solid after heating – that’s denaturation!– Think about how a curling/straightening iron, or

even just a clothes iron, uses heat to do its job.– Think about what an extreme fever can do to

enzymes…yikes.

Protein Structure POGIL

• Yep, it’s a process-oriented guided inquiry learning activity.

• Protein Structure– Note: This one prints funny. Take a look at Page 5

and specifically where the dotted lines are.– Looking at this from home? View the PDF on a

computer screen and you’ll see everything correctly. Print it and some dotted lines become solid for some weird reason.

#3 – ProteinsFinal Note

• Just a heads-up: Many proteins have suffixes of “-in:”– Hemoglobin– Ubiquitin– Transthyretin– Albumin– Insulin

• Friendly hint…move along now…

#3 – ProteinsSummary

• Composition: C, H, O, N• Functional Group(s): Amino group [-NH2],

carboxyl group [-COOH]• Function(s): Enzymes, receptors, structural

components, skin, hemoglobin, antibodies…the list goes on.

• Monomer: Amino acid• Polymer: Polypeptide

#4 – Nucleic AcidsSummary

• Composition: C, H, O, N, P• Functional Group(s): Phosphate group, five

carbon sugar, nitrogenous base• Function(s): Genetic material• Monomer: Nucleotide• Polymer: Nucleic acid (or, rarely,

“polynucleotide”)

#4 – Nucleic AcidsMonomer

• 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 (DNA only)• Cytosine• Guanine• Uracil (RNA only)

#4 – Nucleic AcidsMonomer

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

AdenineThymineCytosineGuanineUracil

#4 – Nucleic AcidsMonomer

• More “scientific”

Aside: 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

#4 – Nucleic AcidsBonds

• 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 a bunch of units later)…

#4 – Nucleic AcidsExamples

• This should be obvious, but the two most important nucleic acids are:– DNA (deoxyribonucleic acid)– RNA (ribonucleic acid)

#4 – Nucleic AcidsSummary

• Composition: C, H, O, N, P• Functional Group(s): Phosphate group, five

carbon sugar, nitrogenous base• Function(s): Genetic material• Monomer: Nucleotide• Polymer: Nucleic acid (or, rarely,

“polynucleotide”)

Closure

• Which one of these things is not like the other?– Glucose, dextrose, insulin, glycogen

• Insulin (protein among carbohydrates)

• Which one of these things is not like the other?– Cysteine, guanine, adenine, thymine

• Cysteine (amino acid among nitrogenous bases)

• Which one of these things is not like the other?– Globular subunit, disaccharide, nucleic acid,

triglyceride• Triglyceride (pseudo-monomer among polymers)