Transcript Chapter 3 Lecture

Chapter 3 Lecture
The Chemistry of Organic
Molecules
Helpful resource
Books on pubmed
Organic Molecules
Functional Groups
4 major classes of these in the
cell, the organic macromolecules
6 classes of these are important in biochemistry
Hydroxyl
Carbonyl
Carboxyl
Amino
Sulfhydryl
Phosphate
Proteins
Nucleic Acids
Lipids
Carbohydrates
Chemical Properties
4 we will concern ourselves with
Solubility
Alkalinity
Reactivity
Structure
Organic Molecules (Compounds)
• Scientists used to believe cells contained something
“extra” that other matter did not; a vital force of some
kind.
• They divided chemistry up into “living” (organic) and
“nonliving” (inorganic) chemistry.
• “organic molecules” were thought to relate specifically to
life processes.
• We now know that the chemical reactions of life are
just like any other chemical reaction.
• The most abundant “life-specific” materials, however, are
carbon and hydrogen.
• Therefore: “Organic molecules” are molecules
containing carbon and hydrogen. Inorganic
Molecules do not.
Matter
Is made of…
Elements
That combine to form…
Molecules & Compounds
Made from a carbon backbone and …
Which Include…
Organic Compounds
Nucleic Acids
Functional Groups
Lipids
hydroxyl
carbonyl
Proteins
Carboxyl
Sugars
Amino Phosphate Sulfhydryl
Which, together with backbone
structure lead to specific…
Hydrophobic
Chemical Properties
Hydrophilic
Acidic
Alkaline
Polar
Nonpolar
Organic Compounds
• Organic Compounds are compounds that contain
carbon and hydrogen.
• ALL complex organic molecules within the cell (the
macromolecules essential to life) are built from the
same basic carbon scaffold.
• What makes them different?
– Carbon skeleton’s structure
– Functional Groups
• Cells contain 4 major classes of organic compounds:
–
–
–
–
Proteins
Carbohydrates
Lipids
Nucleic Acids
• We name organic compounds according to their
functional groups and chemical properties.
Carbon Backbone
• Because of the carbon atom’s unique
structure, it is capable of forming a great
diversity of different structures.
• It is this property of carbon that
contributes to life’s rich diversity on all
levels of the biosphere
Key concept:
FORM FOLLOWS FUNCTION
Show inner life of the cell
Isomers
• A chemical anagram
• Isomers share the same chemical
formula – they are composed of the same
atoms – but have different architecture.
• Form follows function… different shapes
are going to have different functional
implications.
Andrew Ippolito
Warden, I Lit Poop
Isomers of C3H8O
1-Propanol
n-propyl alcohol
H H H
H C C C O H
H H H
Both compounds
have the same
number of C, H,
and O atoms;
however, they are
arranged differently.
2-Propanol
isopropyl alcohol
H
H OH
H C CC H
H HH
Why do they have different names?
We name chemical compounds by how their atoms
are arranged, Because different arrangements have
different chemical effects.
If chemical properties were not affected by the
atomic arrangement, we wouldn’t care about how
they were arranged – and so we wouldn’t have
different names.
Chemical Properties
• The chemical and physical “rules” that
molecules follow due to their unique nature.
• Chemical Properties we will be concerning
ourselves with include:
Solubility (how soluble the molecule is in water)
Alkalinity (measure of how acidic/basic a molecule is)
Reactivity (how likely a molecule is to undergo a
chemical reaction)
Structure (is it long and bendy, clumpy and gooey, or
flat and stiff)
Others?
Solubility
• The ability of a molecule or compound to
dissolve in water.
– Hydrophobic: (phobia) – the molecule is afraid of
water; it does not dissolve.
– Hydrophilic: (phila, love) – the molecule loves water,
and dissolves in it.
• Solubility is influenced by the functional
groups present in an organic molecule
• Molecules are soluble in water if they are polar
(they are imbued with an electrical charge – not
neutral)
– Examples:
Alkalinity (pH)
• Basic concept (no pun intended): pH is really a measure
of how chemically “reactive” the environment is.
– This reactivity depends on two factors
• The hydrogen ion concentration (H+)
• The hydroxyl ion concentration (OH-)
– Why? These are the breakdown products of water.
• Substances that contribute to an increase in the H+
concentration (or a decrease in OH- concentration!) are
considered acidic.
– Example: add HCl to water and the H+ concentration shoots up.
• Substances that contribute to an increase in OHconcentration (or a decrease in H+ concentration!) are
considered basic (or “alkaline”)
Reactivity
• The reactivity of an organic molecule
depends upon the electron configuration of
it’s functional groups.
• Nearly all organic compounds react with
other compounds in one way or another.
Hydration, an example chemical reaction
Functional Groups
– Functional groups are parts of a molecule.
– They have chemical properties that are independent
on what the Rest of the molecule is made out of.
• An arm is an arm, whether it’s on your shoulder or a robotic
car. It still grasps, it still has finger-like appendages.
Functional Groups
– They are not “functional groups” until they are actually
attached to a molecule. If they are free, they are ions!
(wanderers, remember?)
– “hydroxyl ion” “hydrogen ion”, “phosphate ion”, etc.
– Functional Groups contribute to the name of a
molecule (ethane vs. ethanol)
– The functional groups of a molecule influence the
molecules chemical properties.
Functional Groups
Example: [Rest of molecule]—OH
– “OH” is the hydroxyl functional group. When a
hydroxyl group is present in a molecule it increases
the negative charge of a molecule (and therefore
increases its polarity)
– When a single hydrogen in Ethane (C2H6) is replaced
by a hydroxyl group, the molecule ceases to be
ethane and becomes Ethanol (C2H3O).
– Ethane is insoluble in water because it is
hydrophobic, but ethanol, because of its
polar hydroxyl group, is hydrophillic.
– An abbreviation for ethanol in chemical “shorthand” is
EtOH.
The Big Four
Carbohydrates
Proteins
Lipids
Nucleic Acids
Concept: Monomers vs.
polymers
monomer
polymer
Monomeric compounds
Polymeric compounds
Macromolecules
• Macromolecules can be thought of as chains of
smaller molecules.
– Each link in the chain is called a monomer.
– The chain itself is called a polymer.
• Organic macromolecules found in all living cells
are classified into 4 groups:
–
–
–
–
Proteins
Nucleic Acids
Lipids
Carbohydrates
The 4 Major Biological
Macromolecules
• Sugars
– Can be monomeric (monosaccharide) or polymeric
(polysaccharide).
• Lipids
– Any organic, fat-soluble (hydrophobic) molecule.
Highly diverse family of molecules broken down into
further classifications.
• Proteins
– One or more polypeptide chains composed of amino
acids, folding into complex structures
• Nucleic Acids
– Chains of nucleotides or deoxynucleotides.
Carbohydrates
• Two types: simple + complex
• Simple:
– A carbon backbone with a ratio of C:H:O of 1:2:1
(usually, not always).
– simple sugars are called monosaccharides, and are
universally used as immediate energy source to cells.
– two simple sugars can link together by dehydration
reactions to produce disaccharides
Carbohydrates
• C6H12O6 (generic hexose) is the simplest sugar
(monosaccharide) we will deal with right now.
– This compound has 3 different, common structures of its carbon
backbone (isomers).
– these are GLUCOSE, FRUCTOSE, AND GALACTOSE.
– Different pairs of these produce the variety of disaccharides:
• Glu + Glu = Maltose (used in brewing)
• Glu + Fru = Sucrose (table sugar, made in plants)
• Glu + Gal = Lactose (milk)
• plants transport sugars in the form of disaccharides
The common isomers of Glucose (6-carbon monosaccharide)
link
Carbohydrates
• Polysaccharides are long chains of monosaccharides.
• POLYSACCHARIDES are used for two things:
– storing energy in the short-term (they don't freely enter a cell
membrane), and
– structural components (crab shells)
• Energy Storage Polysaccharides:
– Starch = Plants
– Glygoen = Animals
– Both are polymers of glucose; not fructose or galactose.
Carbohydrates
• Starch can either be branched or unbranched in plants. In animals,
it is always branched.
– Unbranched starch (only in plants) is called amylose.
– Branched starch (in plants) is called amylopectin.
• Glycogen is HIGHLY branched compared to amylopectin.
• The shape of these polysaccharides is helical. This allows the
connecting bonds to stick out in the environment, where enyzmes
have access to break them.
• Glycogen's release depends on hormones. insulin from the
pancreas promotes the storage of glucose as glycogen.
Figure 3.8aa
Figure 3.8ba
Lipids
• Lipids: a diverse class of organic
compounds that all share the same
general chemical property: they are
insoluble in water.
– Lipids are made from 2 subcomponents:
• Glycerol (3 carbons with 3 OH groups; an alcohol)
• Fatty acid (a hydrocarbon chain with a carboxyl
group at the very end)
Lipids
• Lipids store more energy than sugars per unit mass.
They are more “energy dense”
• CH bonds (predominant bonds in lipids) are stronger
than CO bonds (predominant bonds in sugars)
– Why? Oxygen’s hogging the electrons, so the bond is weak.
• This is why sugars are used as “fast energy” molecules –
the bonds are much easier to break than lipids!
• Why are saturated fats worse for you than Unsaturated
fats?
– Circulatory disorders. Solids at high temperatures clog your
arteries
• Website: The Lipid Library
Lipids
• Triglyceride: A compound consisting of
1 glycerol attached to 3 fatty acids
• Triglycerides are the subunits of fats and oils.
– Fats have triglycerides containing fully saturated fatty
acids.
– Oils have triglycerides containing unsaturated fatty
acids – those containing double carbon bonds at
various places along the chain.
Lipids
• Fats are solid because their fatty acids are saturated
with hydrogens, making the hydrocarbon chains linear.
– Linear chains stack on each other in a highly ordered way
• Oils are liquid because their fatty acids are unsaturated,
meaning that some carbons in the hydrocarbon chain
are double bonded to each other – not hydrogen. This
bond creates a kink in the chain.
– Kinks allow a greater amount of movement in the chain, and are
therefore less ordered, keeping them in a looser, liquid
configuration
• Solid fats in your blood vessels inhibit blood flow.
Triglyceride
Glycerol
C—O—C
Fatty Acid
C—O—C
Fatty Acid
C—O—C
Fatty Acid
Fat
Glycerol
C—O—C
Saturated
C—O—C
Saturated
C—O—C
Saturated
Oils
Glycerol
C—O—C
Un
C—O—C
Un
C—O—C
Un
Lipid Droplets
• Lipid droplets are the lipid storage organelles of
all organisms.
• Their important role in cellular and organismic
energy storage becomes most prominent in
cases where lipid droplet biology is
misregulated.
– This is for example the case in several major
lipid storage diseases such as atherosclerosis,
diabetes or obesity.
• For a long time it was thought that lipid droplets
only act as storage depots.
• More recent data, however, support the idea that
lipid droplets are highly dynamic organelles
which participate in several cellular
processes and interact with various other cellular
compartments.
Lipid Droplets
• Despite their multifariousness of functions, all
lipid droplets share a simple, stereotyped
structure of a hydrophobic core built of the
storage lipids (mainly triacylglycerols),
surrounded by a phospholipid monolayer to
which numerous proteins are attached (Fig. 1).
• Although the central role of lipid droplets for
energy storage was demonstrated, little is
known about their cellular biology such
as biogenesis, mechanism of protein
association or size and number control
inside cells.
Phospholipids
• Phospholipids
– Heads that dissolve in water and tails that
don’t.
• If left to their own devices in an aqueous
solution, they will move around and align
such that the heads are all facing the
same way, and the tails are all facing the
other way.
++++++++++++++++++++++++++++++++++++
---------------------------------------------------------------P
P
P
P
P
P
P
++++++++++++++++++++++++++++++++++++
---------------------------------------------------------------P
P
P
P
P
P
P
The Plasma Membrane
a.k.a. The Lipid Bilayer
Outside of the cell = Extracellular Environment
Outer Leaflet
Intermembrane Space
Inner Leaflet
Inside the Cell: Cytoplasm
THE SAME IS TRUE FOR MANY OTHER MEMBRANES
Nucleus, Endoplasmic Reticulum, Golgi Apparatus, etc.
• Phospholipids are constructed the same
way as triglycerides, except a single
phosphate functional group replaces a
fatty acid.
Phospholipid
O
C—O—P O R
C—O—C
CCCCCC
Glycerol
Glycerol
O
O
C—O—P O R
C—O—C
CCCCC
C—O—C CCCCCCC
Saturated
C—O—C
CCCCC
C—O—C CCCCCCC
Saturated
O
Steroids
• Characterized by their structure:
• 4 Fused Carbon rings
• What makes steroids different from each
other?
• The function groups attached to the
carbon rings.
Basic structure of many steroids
Beethoven Pneumonic: SIX SIX SIX FIIIIVE
Cholesterol
• A basic steroid that serves as both a structural
component and a precursor for more complex
steroids.
• When inserted into a plasma membrane, cholesterol
increases a plasma membrane’s rigidity.
– Think of a stabilizing fin in a boat.
• Diets high in both cholesterol and fats lead to a build
up of solid material in the blood vessels, leading to
all sorts of trouble!
Membrane in a gel state
with straightened chains.
The green chains are
hydrocarbons, the blue
elements are cholesterol,
and the red spheres are the
head-group atoms of the
lipids. The cholesterol is
removed to show the lipid
chains more clearly in the
visualization on the right.
Membrane in a fluid state.
Unlike the membrane in a
gel state, the membrane
in a fluid state has a low
cholesterol concentration
(one cholesterol molecule
to 16 lipid molecules), and
the hydrocarbon chains
appear highly disordered.
The cholesterol is
removed in the
visualization on the right.
Website
Sex Hormones
• Cholestrol is also precursor to:
– Testosterone = Testes; Estrogen = Ovaries
• Primarily – not exclusively! There are other places
these are formed…
Figure 3.13a
Wax
• Whereas a triglyceride is a small alcohol
(glycerol) attached to 3 fatty acids, waxes
are a long alcohol with a very long fatty
acid.
• Waxes = Long fatty acids + long alcohols
Wax
• Cuticle in plants decreases water loss
• Skin and fur maintenance.
– Earwax has cerumin, which repels or kills insects!
– Traps dust & dirt before it reaches the eardrum
• Bees make a honeycomb to store the
breakdown products of sucrose
– Remember sucrose is a disaccharide of glucose and
fructuose
Proteins
• Proteios, “first place” – the most important
organic molecule in the cell
• Also the most diverse
• As much as 50% of the dry weight of cells
is protein
• Over 100,000 identified so far
Protein Functions
•
•
•
•
•
•
Support
Enzymes
Transport
Defense
Hormones
Motion
Amino Acids
• Points of confusion:
–
–
–
–
Amino acid
Peptide
Polypeptide
Protein
• Additional reading
• Amino Acids are the building blocks of proteins.
• Peptides are two or more amino acids joined
together by a peptide bond.
• Polypeptides are chains of peptides.
Peptide Bond Dynamics (Draw it)
Dehydration
Hydrolysis
H2O
Amino Acids
• The stupid picture in the book
Important Amino Acids
• Phospho-acceptors (can be phosphorylated)
– Serine
– Threonine
– Tyrosine
• Highly charged
– Glutamic Acid (acidic)
– Aspartic Acid (acidic)
– Histidine (basic)
• Structurally Important
– Alanine
– Glycine
– Proline
(3.16 has stupid mistake)
Protein Structure
• Primary structure (“what is the protein’s
sequence?”)
– The sequence of amino acids in the polypeptide chain
• Secondary (the “local” structure of a portion of
the polypeptide chain)
– Stretches of amino acids will tend to form repeating
units such as helices, sheets, fingers, etc.
• Alpha helix
• Beta pleated-sheet
• Zinc finger
– Reinforced by hydrogen bonding
Protein Structure
• Tertiary
– The global shape of the entire polypeptide chain.
Usually classified as “globular” and “filamentous”.
– Globular polypeptides have hydrophobic centers for
the same reason that phospholipids form a bilayer; it’s
the net sum of all forces on the molecule that causes
them to spontaneously settle into a stable structure.
In this case, the polar areas of the chain will react
with the surrounding aqueous environment, while the
hydrophobic regions will aggregate towards the
inside. Thus, “hydrophobic interactions” are truly a
misnomer.
– Reinforced inter-chain crosslinks (disulfide bonds)
Protein Structure
• Quaternary
– When multiple polypeptide chains (that
have their own tertiary structure) come
together and interact in a stable
complex, they will exhibit a higher order
structure called Quaternary structure.
– Short version: The overall shape of 2 or
more polypeptide chains interacting with
each other.
Protein Nomenclature
• A protein consisting of a single polypeptide chain is said
to be a monomeric protein (or simply (“monomer”)
• Proteins with two polypeptide chains are dimeric
proteins (“dimer”)
– Each polypeptide in a dimeric protein is generally refered to as a
subunit
• There are trimeric (trimer), quatrameric (quatramer),
etc… proteins.
• Proteins with many subunits are called multimeric
proteins (multimer)
– DNA and RNA polymerase complexes, nuclear pores, ion
channels, and many gene regulatory proteins are multimeric
protein complexes.
Denaturation & Aggregation
• Denaturation: When a polypeptide’s
tertiary struture collapses (melts)
• Aggregation: when a polypeptide does
not fold properly, but jumbles into a mess.
• Watch video?
Chaperones
• Not all proteins can form their proper
shapes spontaneously. Many need help
as they are being synthesized.
• Proteins that help other proteins fold
correctly are called protein chaperones.
• Proteins that incorrectly fold can form
huge, clumpy messes called protein
aggregates.
Nucleic Acids
• Polymers of nucleotides
• Nucleotides are compounds composed of
three modules:
– Phosphate
• phosphoric acid
– A pentose sugar
• sugar with 5 carbons
– A nitrogenous base
• A nitrogen-containing molecule having the
chemical properties of a base
• The 3rd component, the base, is either a
purine or pyramidine.
Purines are bigger than
AG
pyramidines
T C
Nucleic Acids
• Nucleotides are found as
– polymers DNA and RNA, which serve as
information carriers
– monomers as coenzymes and energy
carriers (ATP)
• Coenzymes are essential factors that ensure
enzymes can carry out their biochemical functions
The Rules
•
•
•
•
•
AT
GC
So, one big always binds with one small
A and T form 2 hydrogen bonds
G and C form 3 hydrogen bonds
– GC is therefore harder to pull apart than AT
• Why?
A
G
A
G
A
G
A
A
T
C
Why does A
always pair
with T, and
G always
pair with C?
T
C
T
C
T
T
So the helix
is of uniform
thickness
Uracil
adenine
Thymine
cytosine
guanine
Benzopyrene, the major mutagen in tobacco smoke, in an adduct to DNA.[52]
Nucleic Acids
• Deoxyribonucleic acid (DNA)
– Very stable molecule.
– Primary function is to store information, such as the primary sequence
of proteins
• Ribonucleic acid (RNA)
– Not as stable as DNE
– RNA does many things. Different classes of RNA are specialized to
their own tasks. The two most characterized are:
• Messenger RNA (mRNA) encodes a protein sequence
• There are transfer RNAs (tRNA) specific for each of the 20 amino acids
• rRNA (ribosomal RNA) is an essential component of Ribosomes, which
help translate the language of Genes to the language of Proteins.
– Each kind of RNA has its own kind of genes. The genes we normally
talk about are actually genes that encode mRNA.
Homework 9 / 18
• Do the multiple choice questions at the
end of Chapter 3.
– Check your answers. Send me or bring to
class those you got wrong.
• Read Chapter 4. E-mail questions.
• We will be doing Lab 1 either Tuesday or
Thursday of next week. BE PREPARED.