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UNIT 2
BIOLOGICAL CHEMISTRY
ORGANIC MOLECULES:
Molecules composed of a carbon skeleton
Monomers: single building units
Polymers: (macromolecules)
Very large molecules composed of many monomers
put together.
Artificial polymers:
Plastics, nylon, Teflon, orlon, polypropylene,
FOUR MAIN GROUPS OF BIOLOGICAL ORGANIC COMPOUNDS
1. Proteins (amino acids) CHONS
2. Lipids (Fats, oils) CHO
3. Carbohydrates ( sugar, starch, enzymes) CHO
4. Nucleic Acids (DNA, RNA) CHONP
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CARBON SKELETONS AND ISOMERS
Isomer:
Compounds w/ the same molecular formula but
different structural formulae
3 isomers of pentane C5H12 ( molecular formula)
STRUCTURAL FORMULA
FUNCTIONAL GROUPS
Clusters of atoms that act in specific ways no matter what
the rest of the molecule is like. OH
Carboxyl group R-COOH C--C=O
Found in amino acids and fatty acids
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Amine group --NH2
H
---N H
Amino Acid bond between carboxyl group and amine group
+ H2O
Amino acids are the basic building block of proteins.
Other important functional Groups:
-OH alcohol
Condensation rxn : two molecules are joined… one loses H
and the other –OH . This is how polymers are made
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(HYDROLYSIS)
Monomer-H + HO—Monomer --
Monomer---monomer + H2O (CONDENSATION )
CONDENSATION REACTIONS ARE REVERSIBLE. WHEN THEY
BREAK UP IT IS CALLED A HYDROLYSIS RXN.
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I. LIPIDS: ( fats, fatty acids, oils , phospholipids,
steroids)
Characteristics :
- Nonpolar
- Don’t dissolve much in water
Elements: C,H,O
Uses: (3 main)
1. Waterproofing
2. Energy storage( contain more than twice as
much as carbohydrates
10g of fat vs 20g of sugar
3. Insulation :
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[Link] Acids
These are the simplest Lipids
Def: A simple lipid molecule composed of a
long hydrocarbon chain w/ a carboxyl group at
one end .
a. Saturated Fatty acids:
All single bonds . ( holding as many H as they can)
b. Unsaturated fatty acid:
Double and/or triple bonds between C atoms
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Trans vs. Cis fats
Hydrophilic :
Water loving
Hydrophobic:
Water fearing
-The Carboxyl end of a fatty acid is polar and therefore
Hydrophilic.
-The hydrocarbon chain end however is hydrophobic
because it is non-polar.
These characteristics make fatty acids an integral part
of cell membranes.
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Fatty acids found where?
1. Cell and organelle membranes
2. Glycolipids ( Carbohydrate + lipid)
3. Lipoproteins ( fat + protein) see book diagram
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[Link] AND OILS: Pg 39 Fig 3-5
Function:
Store energy (energy reserve)
Formed by condensation rxn of 3 fatty acid molecules
to the alcohol ( glycerol ) ( triglycerides)
Fats: solid @ room temperature
Oils: liquids @ room temperature due to more
unsaturated fatty acids.
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[Link] Pg 39 Fig 3-6
Similar to fats except that one or more fatty acids are
replaced by a phosphate group.
Function: pg 39
-structural molecules
- chief lipid component of biological membranes
- polar – nonpolar
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D. STEROIDS: ( HAS A CYCLIC 4 CARBON RING )
Qualify as lipids because insoluble in water
-Cholesterol is the most abundant steroid
- important component of (animal) cell membranes
- involved in vitamin D production
-Hormones
Chemical messengers between different parts of the
body.
Produced in ( adrenal and pituitary glands)
Ex. Cortisone and produced in adrenal
sex hormones in sex organs
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II. CARBOHYDRATES:
Sugars, Starches, and related compounds
FUNCTION:
1. Energy + energy storage
2. Some structural : cellulose in plant
Glucose cell walls ,
Chitin – insect, crustacean, arachnids
Exo-skeletons
A. Monosaccharides:
(Means one sugar)
- These are simple sugars
- Glucose, Fructose ( know structure of
glucose)
- These are monomers of larger carbohydrates
Note: two monosaccharides are called a di-saccharide
Two sugars Sucrose = 2 glucose molecules
B. Polysaccharides:
- Polymer of monosaccharides
Three important forms of polysaccharides
1. Glycogen : animal
2. Starch : Plants
3. Cellulose: Plant cell walls
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A. Glycogen :
- This is the major Animal storage molecule
- Liver + muscles remove glucose in the blood
and assemble it into glycogen to be later
broken back down into glucose for energy.
B. Starch: Pg 42
- This is the energy storage molecule in Plants
- Starch is made up of 2 kinds of glucose
o 1. Amylose
o 2. Amylopectin
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Amylose consists of
a linear, helical chains
of roughly 500 to
20,000 alpha-D-
glucose monomers
linked together
through alpha (1-4)
glycosidic bonds.
Amylopectin
molecules are huge,
branched polymers of
glucose, each
containing between
one and two million
residues. In contract
to amylose,
amylopectin is
branched. It contains
numerous amylose-
like chains of up to 30
glucose residues
linked through alpha
(1-4) bonds,
connected to one
another through alpha
(1-6) branch points.
C. Cellulose
- Most abundant organic material on earth
- Made of long straight chains of glucose
- Cell walls of plants.
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Chitin :
i. Structural polysaccharide in arthropod
exoskeletons and fungus cell walls
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III. NUCLEIC ACIDS
- These include the largest biological
molecules
- Contain CHONP
- There are two kinds of nucleic acids
- DNA, RNA, ATP, ADP, AMP
A. Deoxyribonucleic acid
1. Contains organisms genetic material
Information for making proteins
How to make other nucleic acids
B. Ribonucleic acid
1. Directs the building of proteins
Both DNA and RNA are named after the sugar they contain.
1. Ribose: Ribonucleic acid
2. Deoxyribose: Deoxyribonucleic acid
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DNA is double stranded while RNA is single stranded
Nucleotide: Monomer of nucleic acids
Contains:
1. Sugar ( 5 carbon)
2. 1-3 phosphate groups (PO4-3)
3. Nitrogenous base
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BASES FOUND IN DNA
1. Adenine
2. Guanine
3. Cytosine
4. Thymine
BASES FOUND IN RNA
1. Adenine
2. Guanine
3. Cytosine
4. Uracil
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[Link]
-Proteins make up more than 50% dry weight of
animals and bacteria.
-(Hair, fingernails are made of fibrous protein:
collagen)Collagen is the most abundant protein by
mass in animals.
-Hemoglobin is an oxygen carrying protein
- The most numerous class of proteins are the
enzymes. ( end in –ase)
Enzymes: speed up chemical reactions
Monomer of Proteins:
Amino acid : 20 common amino acids
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The 20 amino acids encoded by the genetic code are:
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Amino acids are attached by Covalent bonds called
Peptide bonds : formed during the condensation rxn.
Dipeptide :
2 amino acids
Polypeptide:
Long string
100-300 amino acids
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Protein:
Def: a functional unit composed of one or more
polypeptide chains.
PROTEIN STRUCTURE
Proteins are long unbranched chains of Amino acids
There are four levels of protein structure
[Link] structure
[Link] structure
[Link] structure
4. quaternary structure
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[Link] Structure: is the sequence of amino acids in
the polypeptide chain ( help by peptide bonds)
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[Link] structure: (hydrogen bonding)
Is the localized structure caused by hydrogen
bonding across a polypeptide chain.
Secondary Structure of a Protein or Polypeptide
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[Link] Structure of a protein
4 Interactions effects these
1. Ionic bonds
2. Hydrogen bonds
3. Disulfide bonds
4. Hydrophobic interactions
Nonpolar sections are pushed together by
Water
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[Link] structure: defined by the way the
polypeptides fit together(fig 3-19 pg 47)
When polypeptides lose their shape their
function and structure are destroyed and they
are said to be Denatured : (caused by heat or
chemicals )
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Insulin
ENZYMES:
All enzymes are proteins
1. Proteins act as biological catalysts.. that is they speed up
chem. Rxns. (lower activation energy)
- Substrates:
The reactants in an enzyme-catalyzed rxn
are called substrates
- Enzymes are named according to their
substrates and the rxns they catalyze.
Ex. RNA polymerase , Sucrase, Lipase
-Over 2000 known enzymes
-Some carry out condensation + hydrolysis rxns
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Enzymes combine w/ very specific substrate in what is known
as lock and key fit
-Enzyme combines w/ substrate and holds it in the correct
angel for the rxn to occur. When rxn over the substrate is
released and the enzyme can be reused. ( note: enzymes are
reuseable)
-The substrate binds a a site called the ACTIVE SITE
A small groove formed as the protein folds. It recognizes the
substrate by its primary structure of amino acids.
-Specific point to point connection.
-The active site is not rigid but flexible
- The size , shape, and electrical charge of the aminoacids R
groups are what help identify and fit the substrate at the site.
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-The active site flexes slightly upon connection known as
“induced fit model”. ( more accepted than lock and key)
Co-factors: Inorganic ions that bind to the enzyme to help
catalyze the reaction
Co-enzymes: Organic molecules (not proteins)
-generally are bound at the active site and the
enzymatic rxn will not work w/o it.
Coenzymes are found in small con. Because they are
reusable. (vitamins, nucleotides, NAD)
NOTE: coenzymes and cofactors are needed in some active
sites for enzymes and substrates to bind.
FACTORS EFFECTING ENZYME ACTIVITY:
1. Concentration of substrate present
2. Inhibitors:
Decrease an enzymes rxn rate.
a. Some bind to active site ( competition)
b. Some disrupt enzymes 3 dimens. Structure and
destroy its function.
3. Temperature: (denatures the protein if too high)
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Generally temperatures above 60o denature
enzymes.
4. pH: pH acids change the shape of the enzymes 3
dimensional structure because H+ ion changes overall
charge of the molecule and disrupts ionic and hydrogen
bonding interactions. (optimum pH for living systems?)
Pg 51 ALLOSTERIC ENZYMES (ALLOSTERIC INTERACTIONS)
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Allosteric Enzymes:
Enzymes that can exist in two or more different shapes
-Allosteric enzymes have
1. Active site
2. Regulatory site
When molecules bind to the regulatory site, it
alters the enzymes shape and therefore its
activity.
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ALLOSTERIC INHIBITORS:
Molecules that when bound to the regulatory site
cause a change in the active site so it doesn’t function
anymore.
Stimulatory molecules: when attached to the R.S. correct the
shape of the active site and let the rxn occur.
Allosteric feedback loop: ( negative feedback loop)
Often the beginning enzyme is allosteric and the final
substrate product is the inhibitor for the regulatory site
on the allosteric enzyme.
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Enzyme 1 --- product 1C------ Product 2C-- Product 3c----
Enzyme 2 Enzyme 3
Allosteric inhibitor
Product 4c------ Product 5C --- Product 6C (glucose)
Enzyme 4 Enzyme 5
Glucose becomes the allosteric inhibitor for enzyme 1
SIMPLE PROTEINS: on hydrolysis include only amino
acids:
1. Albumins - soluble in water (distilled),
most enzymes
2. Globulins - soluble in dilute aqueous solutions;
3. Protamines - not based upon solubility; small
MW proteins with 80% Arginine & no
Cysteine
4. Histones - unique/structural: complexed w
DNA, high # basic aa's - 90% Arg, Lys, or
His
[Link] = high Glycine, Proline, & no Cysteine
when boiled makes gelatin
Keratins - proteins of skin & hair high
basic aa's (Arg, His, Lys), but w Cys
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Complex Proteins:
on hydrolysis yield amino acids + other
molecules
lipoproteins - (+ lipids)
blood, membrane, & transport proteins
glycoproteins - (+ carbohydrates)
antibodies, cell surface proteins
nucleoproteins - (+ nucleic acids)
ribosomes & organelles
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