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Chemistry 1002 Chapter 15Biochemistry |
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Introduction
Biochemistry is an infant science. Many people trace
its birth to the awarding of the Nobel Prize in 1962 to Watson
and Crick for determining the structure of DNA. This event can
be interpreted as a sign of recognition by Nobel committee that
the scientific community had finally broken through the age-old
conceptual barrier that man was fundamentally incapable of creating
and mastering physical life. Many scientists turned their attentions
toward the arduous uphill climb that mankind must now undertake
to make the goal of mastering life a reality, and a bold new field
was born.
The chemistry of life is incredibly complex, but slowly,
bit by bit, science is starting to unravel it. The release and
public reaction to the movie "Jurassic Park," rather
than the 1962 Nobel Prize, is probably the watershed event where
the general public grasped the significance of biochemistry the
way that the scientific community did in 1962. The recent successful
cloning of a sheep by Scottish biochemists has certainly reinforced
this awareness.
This chapter will merely scratch the surface of even
the relatively small amount which is already known about the chemistry
of life. More than anything else you encounter in this course,
the material in this chapter will become more and more familiar
to you as biochemistry advances and changes the way we live our
everyday lives. The time is slowly coming when we will all undoubtedly
live in a very brave new world.
Biopolymers
With the exception of water (70% of human body weight),
fat, and bone, nearly all of the material composing the bodies
of all living beings is polymeric.
Fat made mostly are triesters of glycerol and fatty
acids.
Almost all biopolymers in living beings come in one
of three varieties: carbohydrates, proteins, and nucleic acids
(all are condensation polymers).
Carbohydrates made of simple sugar molecules ("monosaccharides").
Carbohydrates can be monomers, oligomers (very small polymers),
or polymers ("polysaccharides"). The polymers can be
linear, branched, or crosslinked. Examples of carbohydrate polymers
are wood (cellulose), starch, paper, glycogen (blood sugar stored
in liver by insulin), cotton, and fruit pulp. Common dimers (oligomers)
are table sugar and milk sugar. Monomers: blood sugar (glucose)
and fruit sugar. Carbohydrates composed entirely of C, H, and
O. All have empirical formula (CH2O)n,
which is the source of the word "carbohydrate" (hydrated
carbon).
Proteins made of "amino acid" monomers.
Amino acids have both amine functional group and carboxylic acid
group attached to same carbon. All proteins made of C, H, O,
and N, but most also have S. Common protein materials: organs,
muscle, body covering (skin/hair/nails), enzymes.
Nucleic acids are complex polymeric molecules which
store and translate genetic information (DNA and RNA). Name derives
from fact that nucleic acids found mostly in nucleus of cells.
The monomers which nucleic acids are made from are called "nucleotides."
Nucleotides composed of three different molecular units covalently
bonded together: a 6-carbon sugar ("ribose"), a phosphate
functional group, and a "nitrogenous base." The nitrogenous
bases contain at least two nitrogen atoms in either one or two
rings. There are two different kinds of nucleotides. Deoxyribonucleotides
make up DNA and ribonucleotides make up RNA
PROBLEM 8.
What functional groups present in all amino acids?
@ amine group and carboxylic acid group.
PROBLEM 16.
Molecular structure of enzymes related most to which
biopolymers?
@ proteins
PROBLEM 12.
Pick the biochemicals which are polymers and name the
monomers of these polymers.
@:
| Polymer
| Monomer
|
| starch
| glucose
|
| cellulose
| glucose
|
| protein
| amino acids
|
| DNA
| deoxyribonucleotides
|
| RNA
| ribonucleotides
|
Carbohydrates
Monosaccharides & disaccharides
Alpha & beta linkages
Starch, glycogen, cellulose
1,4 Propogation & 1,6 branching
Cotton & nylon
PROBLEM 3.
Name a polysaccharide that is made of only a-D-glucose
and a disaccharide made of both a-D-glucose
and b-D-glucose.
@ amylose and maltose, respectively
PROBLEM 4.
Diff. between amylopectin & glycogen?
@ glycogen is bigger and more highly branched than
amylopectin.
PROBLEM 5.
Function of glycogen?
@ Medium-term energy storage. Broken down ("hydrolyzed")
to glucose (blood sugar) by liver and released into bloodstream
when blood sugar is low.
PROBLEM 6.
Diff. between amylose & cellulose?
@ Amylose smaller, water-soluble, made of a-D-glucoses.
Cellulose larger, not water-soluble, made of b-D-glucoses.
PROBLEM 7.
Why cotton absorb water better than nylon?
@ 1. Cotton (cellulose) has more
H-bond acceptors (OH groups) per carbon (one for every two
carbons) than cellulose (cellulose has one C=O group as H-bond
acceptor for every 6 carbons).
2. It easier for water to interrupt cross-chain H bonding in
cellulose than in nylon (cross-chain H bonds more water-soluble
in cellulose).
PROBLEM 15.
Why can't we digest cellulose?
@ Our enzymes cannot hydrolyze a b
link connecting sugar monomers.
PROBLEM 38.
Identify pictures of a-D-glucose
and of b-D-glucose.
@ a-D-glucose is on the
left and b-D-glucose is on the right.
Proteins
Monomers called a-amino
acids. The alpha here has different meaning than it does in carbohydrates.
Here it refers to the alpha carbon which functional groups are
attached to. Both amine group and carboxylic acid are attached
to the alpha carbon.
Only use term "amino acid" to refer to monomer.
Use term "peptide" to refer to oligomers & polymers
of amino acids, ie. dipeptide, polypeptide. (Memory aid: peptic
acid, Pepto-Bismol)
How make peptides from amino acids?
PROBLEM 1.
Show dipeptide of alanine.
@:
What other sidechains ("R" groups) found
in natural amino acids? Which amino acids are "essential"
(cannot be synthesized by human biochemistry-must be eaten in
protein in diet)?
PROBLEM 2.
What's an essential amino acid?
@ One which human body cannot manufacture. It must
be obtained by digesting (depolymerizing) a protein containing
the essential amino acid.
Protein Structure
Proteins as enzymes act like tiny molecular "hands,"
recognizing individual molecules, selecting only specific molecules
from the zillions of different kinds zinging all around them in
solution, manipulating these molecules, and mashing them together
with other specific molecules to enable chemical reactions to
happen which wouldn't ordinarily happen on their own.
How do proteins recognize specific molecules and maipulate
them in such intricate ways?
Key to this enigma involves structure.
Proteins have four levels of structural control which
enables them to create exact shapes which fit "substrate"
molecules exactly. Multiple possible structures for a protein
give it multiple shapes which it can use for manipulating molecules.
These levels of structure are known as primary, secondary,
tertiary, and quaternary (1º,
2º, 3º,
and 4º).
Primary structure is the sequence (order) in which
amino acid monomers are covalently bonded together (via "peptide
bonds") to create the polymer.
Secondary structure is the structure or shape which
the polymer acquires when it changes its shape ("folds"
is terminology used) and creates hydrogen bonds between N-H donors
and C=O acceptors in same protein molecule. Secondary
structure does not involve sidechains-"backbone" only.
Tertiary structure causes even further refinement of
the shape of a protein. It can also involve N-H to C=O hydrogen
bonding, but not using atoms on the backbone. Tertiary structure
involves only sidechain groups. Other kinds of attractions
can make sidechains from amino acids on different parts of protein
stick together (besides hydrogen bonding):
1. Sidechains can have opposite electrical charges (one +,
other -).
2. Long catenated hydrocarbon sidechains are "hydrophobic,"
will stick to each other to avoid water.
3. Sidechain of amino acid "cysteine" has a SH functional
group. Two cysteine sidechains can react with one another to
make a "disulfide link". -SH + HS- Æ
-S-S- + H2. Proteins use this reaction to
make crosslinks the way humans do with rubber (remember "vulcanizing").
Involves sidechains in same molecule.
Quaternary structure is what occurs when two or more
different protein molecules stick together to make an "aggregate."
Quaternary structure involves same kinds of sidechain interactions
as tertiary structure (backbone not involved).
PROBLEM 10.
What are primary, secondary, tertiary, and quaternary
structure?
@ Ways proteins have of attaining exact shapes. Primary
is amino acid sequence, secondary involves backbone hydrogen bonding,
tertiary involves sidechain attractions in same molecule, and
quaternary involves sidechain attractions in different molecules.
PROBLEM 11.
In protein what type of bonding holds helical (secondary)
structure in place?
@ Hydrogen bonding.
Show Fig. 15-8 example of helix secondary structure
with hydrogen bonding, then composite structure.
PROBLEM 9.
What type of atom is in all proteins but not fats or
carbohydrates?
@a. Nitrogen (amino groups)
What other type of atoms is a protein likely to have?
@b. Sulfur for disulfide crosslinks (amino acid cysteine).
Coenzymes
Proteins have so many options open to them using only
shape, and amino acids made of C, H, N, O, and S that they can
do almost any kind of organic chemistry which does not require
inorganic atoms (like transition metals).
Sometimes other atoms are required and proteins need
a little inorganic help. When this happens a protein will be
built attached to a small organic fragment containing an inorganic
atom. These fragments, "coenzymes," commonly called
vitamins & minerals.
PROBLEM 13.
What is function of many vitamins?
@ To act as coenzymes.
PROBLEM 24.
Which chemicals can be coenzymes?
@ Vitamins and minerals.
Functions of Proteins
Proteins not only used as enzymes, muscle, organs,
and body covering (hair, skin, nails) in body. Animal cell "membrane"
(envelope which holds contents of cell) made of fat with protein
molecules imbedded for strength. Protein molecules can be attached
to other molecules on inside and outside of cell. A "signal"
(message) molecule can interact with piece of protein on outside
of cell and cause protein to change situation inside cell.
Signalling involves hormones outside & "G proteins"
inside. G proteins involved things like in vision, cell growth,
enzyme production.
PROBLEM 34.
Give function of and three systems which make use of
G proteins.
@ Function to respond to chemical signal originating
outside cell and passed thru membrane by transmembrane protein,
and to pass this signal on to inside of cell. Three examples
of systems which use G proteins are vision, cell growth, and enzyme
production.
Bioenergetics
Every living being on earth uses same identical chemical
molecule to generate immediate energy to stay alive:
ATP + H2O Æ
ADP + H3PO4 + E
A large part of the biochemistry of all plants and
animals is dedicated to assuring that cells can easily maintain
the constant supply of ATP needed to stay alive.
To keep ATP flowing at all times living beings must
all have complex energy storage systems in place. In every animal
cell ATP is manufactured continuously on millions of chemical
assembly lines which use glucose for fuel. The series of biochemical
reactions the cell uses to extract energy from glucose in order
to make the ATP called the "Krebs cycle."
In order to be sure that a constant supply of glucose
is available to keep the ATP production running we keep stores
of glucose polymers in stock (for plants it's starches and for
animals it's glycogen in the liver). These polymers are broken
down to glucose monomers as needed to keep blood sugar levels
(sap sugar levels in plants) up to par.
In order to stretch carbohydrate supply (use slower)
we metabolize fat. Fat makes much more ATP than glucose but fat-metabolism
chemistry doesn't work well without simultaneous Krebs cycle ("fat
burns in flame of carbohydrate").
Question: How long can you live if suddenly lose (can't
replace) all of...? ATP: immediate death
glucose: minutes
glycogen: hours
food supply: month(s)
ATP works by transferring phosphate group to other
molecules, making them unstable, and causing them to do reactions
they wouldn't ordinarily do in order to lose the phosphate group.
Bottom line: typically energy is stored and transferred in the
form of unstable bonds. The energy is released when these bonds
are broken. Exceptions: some oxidation-reduction reactions, photosynthesis,
etc., use other kinds of unstable chemical species.
PROBLEM 21.
How does life store and transfer energy?
@ Mostly in the form of unstable bonds.
PROBLEM 23.
What's the purpose of ATP?
@ To transfer a phosphate group to stable molecules
so that they become unstable and can do otherwise unfavorable
chemical reactions.
Show Krebs cycle, Fig. 15-21.
PROBLEM 14.
Why carbohydrates considered energy-rich?
@ Because when cells oxidize glucose monomers of carbohydrates
to CO2 and water using Krebs cycle enough
energy is liberated to make 36 molecules of ATP per glucose molecule.
PROBLEM 18.
What molecule produces soreness in muscles after exercise?
@ Lactic acid.
Energy From Light
What about light energy from sun? What's all this
about plants getting energy directly from the sun (photosynthesis)?
What does light energy from the sun do that makes us "see"
things, and what's all the fuss about damaging UV light from sun?
Show photosynthesis & vision chem.
PROBLEM 37.
Explain why visible light makes us see and UV light
makes us blind.
@ Visible light has less energy than UV light. Visible
light has just enough energy to break the cis double bond of 11-cis
retinal (a weak bond) but not enough energy to break any other
bonds. UV light has enough energy to break all kinds of bonds,
like the peptide bonds in the protein which the retina is made
of. Trashed retina leads to blindness.
Digestion
Biopolymers are made by condensing out water molecules
from between monomer units to form polymer. Digestion is basically
the reverse of this. It "depolymerizes" biopolymers
making oligomers and monomers ("hydrolysis"). Body
wants to make its own particular polymers, not use same polymers
made by animal we just ate.
PROBLEM 17.
Nature of digestion of large molecules?
@ Break bonds holding components of large molecules
together using water molecules.
PROBLEM 20.
What are the products of complete digestion
of fats, proteins, and carbohydrates?
@ fats: fatty acids and glycerol; proteins: amino acids;
carbohydrates: monosaccharides (or simple sugars).
PROBLEM 22.
What's role of enzymes in digestion?
@ Same as in other reactions; enzymes make them happen
faster and more easily. Digestive enzymes facilitate hydrolysis
reactions.
PROBLEM 19.
Why don't digestive enzymes digest the organs which
produce them?
@ They are produced in inactive form (ie. lack coenzyme).
Enzyme activated in stomach or intestine.
After we break down biopolymers and fats into components,
body uses these to reconstruct similar biopolymers. Some of resulting
biopolymers stored in liver. Liver a lot like factory outlet
warehouse; makes and stores all kinds of carbohydrates (ie. glycogen),
fats, and enzymes so these always available quickly when body
needs them.
PROBLEM 33.
Why is liver called the central nutrient bank of the
body?
@ Liver has all kinds of nutrients stored and ready
to be released into bloodstream when the body needs them.
Nucleic Acids
Condensation polymers based on Deoxyribonucleotide
(DNA) or ribonucleotide (RNA) monomers. DNA: software governing
all biochemistry; RNA: protein production machinery.
DNA Replication
Occurs when growth, healing, etc. requires cell to
divide. DNA must duplicate self so that there are two identical
copies of DNA. This way each of two "daughter" cells
gets a copy for its nucleus when parent cell divides. Errors
in replication of DNA lead to mutations. Cells with mutated
DNA make slightly different proteins than original cells. Other
mutation causes: DNA damage and inaccurate repair, and inaccurate
reproduction of DNA when making sex cells.
Recombinant DNA
Humans now capable of making plants and animals with
"hybrid" DNA synthesized from fragments of DNA acquired
from several different plants and/or animals and recombined
to make new kinds of plants and animals which never existed before
(ie. grapefruits as sweet as oranges)
Comments?
Last Revised : Sunday, October 5, 1997
Copyright © 1997
Louisiana State University, Department of Chemistry.
All rights reserved.
http://www.chem.lsu.edu/lucid/courseinfo/chem1002/ch15.html
