In This Lesson:
Biochemistry
(Lesson 2 of 5)
Today is Wednesday,
October 14th, 2015
Pre-Class:
You remember the four types of organic
molecules, don’t you? DON’T YOU?
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 fightingover 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 slowly…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”).
Carbonyl Group
• Carbonyl = >C=O
• Important Properties
– Polar/hydrophilic.
– Molecules containing it are called ketones if the
group is in the middle; aldehydes if it’s on the end.
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.
• By the way – dimers are pairs of monomers. Makes sense.
– 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.
-OH
Paper
Clips
>C=O
The Lost
Ark
Biebs
• 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.
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 – Carbohydrates
Summary
• 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 – Carbohydrates
Monomers
• 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 – Carbohydrates
Functional Groups
• Remember, -OH (hydroxyl) is the functional
group for carbohydrates.
#1 – Carbohydrates
Disaccharides
• 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 “hydroslices.”
• Sure enough…
Conceptually
• Dehydration synthesis:
H2O
• Hydrolysis
H2O
Molecularly
• Dehydration synthesis:
• Hydrolysis
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 – Carbohydrates
Bonds
• Once the bond has formed, it’s known as a
glycosidic bond, less commonly as a C-O-C
bridge.
#1 – Carbohydrates
Polysaccharides
• 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 – Carbohydrates
Examples
#1 – Carbohydrates
Final Note
• Just a heads-up: Many carbohydrates have
suffixes of “-ose:”
– Maltose
– Glucose
– Fructose
– Sucrose
– Galactose
• Also, the term “glyc-” indicates carbohydrates.
• Friendly hint…move along now…
#1 – Carbohydrates
Summary
• 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 – Lipids
Summary
• Composition: C, H, O (except they’re mostly nonpolar).
• Functional Group(s): Carboxyl [-COOH]...sorta.
• Function(s): Fats, oils, waxes, steroids,
cholesterol, some hormones, pigments…and
energy storage.
• Monomer: Um…
• Polymer: Sigh…
• Lipids are weird. The best thing you can do is
remember that.
#2 – Lipids
Monomers
• 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 group 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 Types
Type
Phospholipid
2 nonpolar fatty
3 nonpolar fatty
acids, 1 phosphate
Structure
acids, 1 polar
group, 1 glycerol
glycerol molecule molecule (polar)
Function
Triglyceride
Storage of energy
Cell membrane
composition
Steroid
4 fused rings plus functional
group
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 – Lipids
Summary
• Composition: C, H, O (except they’re mostly nonpolar).
• Functional Group(s): Carboxyl [-COOH]...sorta.
• Function(s): Fats, oils, waxes, steroids,
cholesterol, some hormones, pigments…and
energy storage.
• Monomer: Um…
• Polymer: Sigh…
• Lipids are weird. The best thing you can do is
remember that.
#3 – Proteins
Summary
• Composition: C, H, O, N
• Functional Group(s): Amino group [-NH2],
carboxyl group [-COOH]
• Function(s): Enzymes, receptors, some
hormones, structural components, skin,
hemoglobin, antibodies…the list goes on.
• Monomer: Amino acid
• Polymer: Polypeptide
#3 – Proteins
Monomer 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 – Proteins
Structure
• Key: Amino acids take an N-C-C central structure.
• Key: The central C has an H on one side and the Rgroup comes off the other.
#3 – Proteins
Monomers
• There are 20 very
different amino
acids found in all
living things
– Plus two found
in Archaea.
• 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
Organic Chemistry Lite
• See that weird ring
shape?
• That’s a carbon ring,
unless other
elements are listed.
• Usually the ring is
non-polar.
#3 – Proteins
Polymers 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 – Proteins
Bonds
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, disulfide bonds, 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, different pH
levels, or salty environments 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 – Proteins
Final Note
• Just a heads-up: Many proteins have suffixes of “in:”
–
–
–
–
–
Hemoglobin
Ubiquitin
Transthyretin
Albumin
Insulin
• Even the word “protein” ends in “-in.”
– “Whoooooooaaaa.”
• Also, amino acids tend to end in “-ine” and
enzymes end in “-ase.”
• Friendly hint…move along now…
#3 – Proteins
Summary
• Composition: C, H, O, N
• Functional Group(s): Amino group [-NH2],
carboxyl group [-COOH]
• Function(s): Enzymes, receptors, some
hormones, structural components, skin,
hemoglobin, antibodies…the list goes on.
• Monomer: Amino acid
• Polymer: Polypeptide
#4 – Nucleic Acids
Summary
• 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 Acids
Monomer
• 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 Acids
Monomer
Guanine
Adenine
Uracil
Thymine
Cytosine
http://www.biologyjunction.com/images/nucleotide1.jpg
#4 – Nucleic Acids
Monomer
• 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 Acids
Bonds
• 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 Acids
Examples
• This should be obvious, but the two most
important nucleic acids are:
– DNA (deoxyribonucleic acid)
– RNA (ribonucleic acid)
#1 – Carbohydrates
Final Note
• Just a heads-up: Nitrogenous bases often end
in “-ine:”
– Thymine
– Cytosine
– Adenine
– Guanine
– Uracil…er…hmm.
• Friendly hint…move along now…
#4 – Nucleic Acids
Summary
• 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”)
Aside: Murchison Meteorite
• Confirmed – 1969 Meteorite Brought Genetic
Building Blocks From Space article
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)